diff --git a/.travis.yml b/.travis.yml
index 728dfa65a2f..c9f20fe2f5c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -29,7 +29,7 @@ jobs:
       script:
         - set -e
         - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git,./deprecated/ .
-        - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list
+        - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories.list
 
     - stage: test
       env: CHUNK=0
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml
new file mode 100644
index 00000000000..e7bf6140bf6
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml
@@ -0,0 +1,13 @@
+categories:
+- Fasta Manipulation
+- Graphics
+- Statistics
+description: Length Distribution chart
+long_description: |
+  This tool creates a histogram image of sequence lengths distribution
+  in a given fasta dataset file.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fasta_clipping_histogram
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml
new file mode 100644
index 00000000000..ca237fe1e08
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml
@@ -0,0 +1,119 @@
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
+    <description>chart</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.49">perl-gdgraph</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+fasta_clipping_histogram.pl
+'$input'
+'$outfile'
+    ]]></command>
+
+    <inputs>
+        <expand macro="fasta_input" />
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="png" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in1.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out1.png" compare="sim_size" delta="512" />
+        </test>
+        <test>
+            <param name="input" value="fasta_clipping_histogram-in2.fa" />
+            <output name="outfile" file="fasta_clipping_histogram-out2.png" compare="sim_size" delta="512" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
+
+**TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
+
+-----
+
+**Output Examples**
+
+In the following library, most sequences are 24-mers to 27-mers.
+This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
+
+In the following library, most sequences are 19,22 or 23-mers.
+This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
+
+-----
+
+**Input Formats**
+
+This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
+
+    >sequence1
+    AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+    >sequence2
+    GTGTGTGTGGGAAGTTGACACAGTA
+    >sequence3
+    CCTTGAGATTAACGCTAATCAAGTAAAC
+
+If the sequences span over multiple lines::
+
+    >sequence1
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
+
+Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
+
+   >sequence1
+   CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+-----
+
+**Multiplicity counts (a.k.a reads-count)**
+
+If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
+
+Example 1 - The following FASTA file *does not* have multiplicity counts::
+
+    >seq1
+    GGATCC
+    >seq2
+    GGTCATGGGTTTAAA
+    >seq3
+    GGGATATATCCCCACACACACACAC
+
+Each sequence is counts as one, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
+
+Example 2 - The following FASTA file have multiplicity counts::
+
+    >seq1-2
+    GGATCC
+    >seq2-10
+    GGTCATGGGTTTAAA
+    >seq3-3
+    GGGATATATCCCCACACACACACAC
+
+The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
+
+.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
+
+Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+.. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa
new file mode 100644
index 00000000000..dab0e10a3e3
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in1.fa
@@ -0,0 +1,10 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa
new file mode 100644
index 00000000000..40fbc313e49
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-in2.fa
@@ -0,0 +1,84 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA
+GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG
+TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA
+ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA
+CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT
+TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA
+AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT
+CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG
+CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC
+CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT
+TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC
+ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA
+AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC
+ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC
+TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT
+ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT
+TCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA
+TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT
+TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat
+ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa
+tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt
+gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag
+tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct
+tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca
+caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA
+CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT
+GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG
+AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG
+AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA
+AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA
+ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT
+CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT
+TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG
+GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA
+ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT
+CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA
+AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA
+TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG
+ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT
+GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT
+ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG
+ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG
+GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT
+GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT
+GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt
+gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt
+tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt
+ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA
+ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA
+GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA
+TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg
+tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt
+ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA
+ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt
+gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT
+GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG
+AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA
+GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA
+AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC
+AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa
+aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc
+ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc
+aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT
+TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT
+GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt
+gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG
+TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT
+TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct
+ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT
+GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT
+TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT
+ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA
+GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT
+AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC
+TTTGATGCCAATCCAACAATTTTGCATATATTA
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out1.png b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out1.png
new file mode 100644
index 00000000000..52c34a07f3e
Binary files /dev/null and b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out1.png differ
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out2.png b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out2.png
new file mode 100644
index 00000000000..0d5c131824a
Binary files /dev/null and b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/fasta_clipping_histogram-out2.png differ
diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/input.fasta b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/input.fasta
new file mode 100644
index 00000000000..042e11fab76
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/test-data/input.fasta
@@ -0,0 +1,6 @@
+>sequence1
+AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
+>sequence2
+GTGTGTGTGGGAAGTTGACACAGTA
+>sequence3
+CCTTGAGATTAACGCTAATCAAGTAAAC
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml
new file mode 100644
index 00000000000..44f7d5b06de
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/.shed.yml
@@ -0,0 +1,10 @@
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+categories:
+- Fasta Manipulation
+description: FASTA Width formatter
+long_description: |
+  This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+name: fasta_formatter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml
new file mode 100644
index 00000000000..efaeb6099d9
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml
@@ -0,0 +1,91 @@
+<tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width">
+    <description>formatter</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <!--
+        Note:
+            fasta_formatter also has a tabular output mode (-t),
+            but Galaxy already contains such a tool, so no need
+            to offer the user a duplicated tool.
+
+            So this XML tool only changes the width (line-wrapping) of a
+            FASTA file.
+    -->
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fasta_formatter
+-w $width
+-o '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="fasta_input" />
+
+        <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Re-format a FASTA file into a single line -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="0" />
+            <output name="output" file="fasta_formatter1.out" />
+        </test>
+        <test>
+            <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="60" />
+            <output name="output" file="fasta_formatter2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool re-formats a FASTA file, changing the width of the nucleotides lines.
+
+**TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
+
+--------
+
+**Example**
+
+Input FASTA file (each nucleotides line is 50 characters long)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
+    CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
+    TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
+    ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+    TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+    aactggtctttacctTTAAGTTG
+
+
+Output FASTA file (with width=80)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
+    ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
+    ATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
+    GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+Output FASTA file (with width=0 => single line)::
+
+    >Scaffold3648
+    AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
+    >Scaffold9299
+    CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/macros.xml b/tool_collections/fastx_toolkit/fasta_formatter/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta
new file mode 100644
index 00000000000..3c76807ab38
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.fasta
@@ -0,0 +1,100 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
+CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
+TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
+GTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTAT
+ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATC
+TACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT
+TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGC
+AAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTT
+GATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATA
+GCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAG
+AAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACT
+AAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT
+TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAA
+AGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAG
+AGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCA
+ACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTC
+GCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATA
+CATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT
+ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATA
+ATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
+TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
+GAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAa
+ggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaag
+ctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatga
+taaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt
+gtttctctcatggtctgtgagagatatagggtagtcccatatacatcttt
+ctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatca
+ttttgatgattccagaaccttgcagatgcgagatggtagatgatcaacct
+tttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccat
+aactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAG
+TTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT
+GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGC
+CAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAA
+AAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGA
+AGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGT
+GTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAA
+ATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT
+CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATT
+AAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGAT
+ATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGT
+GTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATA
+CTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAG
+ATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTA
+TGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAAT
+TTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATT
+AGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTT
+TTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAAC
+GAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT
+ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATC
+GAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAAT
+ACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAG
+TTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAA
+TCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAA
+TGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt
+gataatttttttttctttgataatttttttctttttctttaataaatttt
+ttggataatttttttttggataaatagttcttttttgataattctaataa
+tttttttatttattttttttttttctataattttttttaaaaaatttatt
+aatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGAC
+AATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATAC
+GCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACT
+TTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGA
+TGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtg
+tgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTG
+ATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA
+ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgt
+gcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATT
+GCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAA
+AAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAA
+CGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAG
+AGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA
+AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAA
+GTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtact
+atgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgca
+tttgaaagataatactaatttacaacttccctaaaaaaggtggggcttga
+aaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactt
+tagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAA
+GTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGT
+ACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttat
+atCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctc
+tcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACT
+TGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT
+TTGtctctgttcccctctccccccctctctctctctctctctctctctct
+ctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTG
+TTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTT
+AATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAA
+CTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTA
+CTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA
+GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTT
+CTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTG
+GACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATA
+TTA
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out
new file mode 100644
index 00000000000..dab0e10a3e3
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter1.out
@@ -0,0 +1,10 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACAACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATACATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACATTATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAAAAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATTCTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGGCACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGCCTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCTTCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGCATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTAAACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCCATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGCTACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTTATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGTTCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTTTCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaatttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaatacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaatttgtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatagtgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaaccttgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttcacaatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAACACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATTGTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAGAAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTGAAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAAAACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAAATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATATCGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATTTGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACGGTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAAATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTATCCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATAAACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCATTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATGATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATTGTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCTATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATGATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTGGTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTTGGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCTGCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAtttttttgataatttttttttctttgataatttttttctttttctttaataaattttttggataatttttttttggataaatagttcttttttgataattctaataatttttttatttattttttttttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTAACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAAGACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACATTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtgtgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgtACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATAACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgtgagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCATGAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGGAAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGAGAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAAAAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGCAGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaaaaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttccctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtcaaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTTTGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCTGTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttcttgtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAGTTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTATTTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctctttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTTGCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGTTGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATTATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAAGATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTTAACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGCTTTGATGCCAATCCAACAATTTTGCATATATTA
diff --git a/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out
new file mode 100644
index 00000000000..40fbc313e49
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_formatter/test-data/fasta_formatter2.out
@@ -0,0 +1,84 @@
+>Scaffold3648
+AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCA
+GGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGG
+TATTGTGCATTATATGACCTGTAATACACAGTATAACTTTTCAAATACTTTTGTTTTACA
+ACTTTTCTCTCTGGACTTATATTAAAGTCAATTTTAATGAACATGTAGTAAAAACTAATA
+CATGTACATCTACAGTTTATTTATTTTTTTCTTCTTCTTTTTGTATTTCTTGTGTTACAT
+TATTTCACTTCACGTTCATGTTACCAACCTTGCCCCCTTGCTTTCCATGCAAAAAAAGAA
+AAAAAAGAAGCAATACTTACACTTACCCTTGAGATATCTTGATCTGAATGCTTTAACATT
+CTATATGTACAATAAATTTTTGTATCTATAGCCTATTATTATATATGTTGCTATGTCAGG
+CACATTGACAACATTCTCAGAAGGTTAGAAGATGGTATTGTTCTGAAATGCCTGGAATGC
+CTTGTGAACTAAGATGATTACTCATGTCATTAAAGTCCCCTAACCCAGGTATTTCCTCCT
+TCCCATGACGAAAACAGTCCATTTAAACTTCACCCCACTTTGGACCCGAAAGTGGGGTGC
+ATTTTGGTGGTAAGCTCACCACAGAGCAAGAGAGAGTTAGAGTCCCTAATCTGCAGTGTA
+AACAAACTTTGCCAGGACATCACCAGCCCAACCTTGATAAGTACTGCTTGGAACTCCTCC
+ATGATGTTCTAGTCTTATTCGCAGTCTCATATAGGTTCGGATTTTGTCCATTCTCATAGC
+TACCAGTATACATGGGAGATGCCAGTTTCATCTTCCTTGCTTCACTTTATAAGCATAGTT
+ATATCANGAACTTCCTGGTTATAATTATGTTCCTTTCAAGTTTCATCATAATTGTCTAGT
+TCGATATAGTACATGGACACAATTAAATATGATATTGTCT
+>Scaffold9299
+CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCA
+TAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGGAAAAGCATCCTTGTTTGTT
+TCACTATGCTTTTTAATGGTTGACGTTAAaggtaaagaccagtattggaaacgccccaat
+ttcaaaaaatgaaatggaagctctcattaccaatcatgtgaaagaatatgttttgactaa
+tacatgatgataaaaaaattgccgggaaaccgcctactaattcatatatttagtaaattt
+gtttctctcatggtctgtgagagatatagggtagtcccatatacatctttctgtgtatag
+tgcttgtaactttacgaagaatgggccaaatttcttatcattttgatgattccagaacct
+tgcagatgcgagatggtagatgatcaaccttttctgatcgattccataacgtttctttca
+caatgcaatcgcatgaccataactggtctttacctTTAAGTTGTAGGTCTTAATTGATAA
+CACTATATAGTTTTTTTCTTTTTACTGTTTTTATTAATGACCTCTGTAATTTGCCCTATT
+GTGAAAATACTAAAATATGTTTATACGCCGATGATGCGGCAATATTTTGCCAAGGCAAAG
+AAATTGCCCTTGTTGAGAAAACTCTTAAATGTGAGTTTAAAAAAATAGTTGATCACATTG
+AAAAAGATGACTTAATGTTGAATATCAAGAAGTGTAAGATCATGTTATTTGGGACAAGAA
+AACGAATCAAAAATCAAAGTGTACGCTTGATTTACAGAGATAATGTTATCGAAGTTGTAA
+ATGAATTTAAATATCTTGGTGTATTATTTGATAATTATTTAAAGTGGGATATACATATAT
+CGAAAACTGCCTCCAAAATATCTAGAACCATATCATGTATAAAACGAATTAAATATTATT
+TGCCGAAAAGAATTTTAAAATTGTTATATGATAGTTTGATATTGTCACATATTGACTACG
+GTATTGTTTTGTGGGGATGTTCAGCAAAGTGTCATTTGGAAAAGTTACAAAAGTTACAAA
+ATCGTTATGCCCGTTTAATACTAAACGTAGATATTTTGACACCTCGTATTATATTATTAT
+CCTCTCTAAGATGGCAATCAGTTGTTCAGAGAGTGCAATACCAA
+>Scaffold9309
+GAAGGAAGAAGAGGAAAATAATGATGAATTTGTAGAATTTCTATAACGTATGAAAACATA
+AACAACATGAAAAAGTATGAACCGACAGAAGAATGAAAATTTCAATCATATAACATGTCA
+TTCACTTCTCTTCTCTGACTGTCAAGTATTAGGTATTCCTTTTTATTTCCTCTTAAAATG
+ATCATAGTTTCCTATTTCTTTTACACCATTGGGAAGGGAATTCCAATGTTTTATGGCATT
+GTAATAAAACGAATTTCCAATACTACCTACTCTTTCTGGTAAGTTAAAGTTGAATCGGCT
+ATTTCTTGTATTATAATCATGTACGTCAGTAACAAGATCGAAGTTGGATCGAATATAATG
+ATTCGACCTAGTATGATATATTTTATGCACGTGATGCAATACGAGTTGTTTTGATCTTTG
+GTCGACTTCAAGAAAACCAGCTTTAGAAAGTTCGCTGTAGCCAACATGAGTTCTTGCCTT
+GGACTAGAACAGTTGATAAATCTCACCATTTTGTTCTTTAAGATGGGTAGAAGAATCCCT
+GCAATCTAAATGGTCAATTACTGTGAAGTTATTTTTACTGGATGCACCCAATAttttttt
+gataatttttttttctttgataatttttttctttttctttaataaattttttggataatt
+tttttttggataaatagttcttttttgataattctaataatttttttatttatttttttt
+ttttctataattttttttaaaaaatttattaatttttaattaaaaaaaaaataaGAGTTA
+ACAGATTAAGGGAAACTGACAATTCAAAAAAAAAAAAAA
+>Scaffold9310
+GCGGGGGCTGGGGAGGAAGGGGTGGCGTTATTTCACTTCCGATCTAATACGCTTTCTTAA
+GACACTGAAATATCAGTAGGTATTGGTATAGAGAATTACTTTTTATTTTTAATTAAAACA
+TTATCGAAATGAAGATACAGAGAAAAACGATGAGATGTAAGAAGTGCGCGTATTTAtgtg
+tgtgggtgcgtgtgtgtgtgtgtgtgtgtgttgtgtgcgtgcgtgtgtgtggtggtgtgt
+ACTAATTTTGATGTGTGTTGTGGCACAATTGCAATCATCAGTATCTTCATGAAAATGATA
+ACCAGAAGCACAAAAAGGAGGgtgcgtgtgtgtgtgtgtgtgtttagtgtgcgtgcgtgt
+gagggtgtttaagtgtgtatgtCGGAAATGTGGCACAATTGCAATCATCTGTATCTTCAT
+GAAAATGATAACCAGAAGAACAAAAAAAAAAAACATTGAGAGAACATGTTTTTTTGATGG
+AAGACAAGAAGTTCTCGTAACGTAGGATCTCCGAGACATGATGGGGTCAACTTAAAAAGA
+GAGCAGTGAGAGGCATTTATATCGAAGGTCAGGGAAAGGCAAACAAAGAAAGAAAAAAAA
+AAGGCTCACAGGAGAACGAAAACACGGGCCAAAATAATAAACAGGAGCAAGTGAACGGGC
+AGTTTGGTAGCTACTTCATTTACCGGCTTTTAAaggtactatgtcccatttgcaggtcaa
+aaaaaatgaaaaagttaaattccaactgcatttgaaagataatactaatttacaacttcc
+ctaaaaaaggtggggcttgaaaatgtcttcaagtgcggaaaataacgactattagttgtc
+aaatcgactttagggCTATAGAGCCCAAAAGTAATAGTCTTGA
+>Scaffold11911
+TTCTTGGCACCCCCCCCCCCCCCACACTCCTGCACTGAAGAACTACTCAAGTTTAAACTT
+TGCATTGCTTTTCTTTCTTTTTCAGTATTTTTTGCTTGGTACATGTTTCTCTTAATATCT
+GTCGTATAGatttttaatatttttatttatatCTACGTCAATCTGGCTGttctttttctt
+gtcttctttttttttctctctcttttttttcctcgtattttGTATTGATCCTTACCCTAG
+TTTTTGAACTTGAACAGCAATTTGCAGCACTCAAATTTCTTTAAAATTACCTTCTCTTAT
+TTGtctctgttcccctctccccccctctctctctctctctctctctctctctctctctct
+ttcATCTCCCATATCATAATTTGAAGTACCATCTATGGTGTTTTCAGATTGATCTTTCTT
+GCTTTCCCCACCCTCCCCCTTTATGCAGTTAATTTTCAGTCTATTTGTGTTTTCTGTGGT
+TGATTCTAATCATATTCTAACTCTTATTTTACATTTTACTTCACTAACAACTGGTTTATT
+ATATTTGTTACTAATTTTGAATTAAACTATTTACCATTCTGAACGAACTGAAAGATTAAA
+GATCAAACTATCTATGAATAGAATGGTATTTCTTCAATTTATTCAAATTTCTCTCTCTTT
+AACCCCCTTTTTCTGCTTGCATTTTTATCCCTTTGCCGTGGACTTCACTGGATATTTTGC
+TTTGATGCCAATCCAACAATTTTGCATATATTA
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml
new file mode 100644
index 00000000000..f3c636477ef
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/.shed.yml
@@ -0,0 +1,10 @@
+categories:
+- Fasta Manipulation
+description: RNA/DNA converter.
+long_description: |
+  This tool converts RNA FASTA files to DNA (and vice-versa).
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fasta_nucleotide_changer
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml
new file mode 100644
index 00000000000..54424a9eddc
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml
@@ -0,0 +1,75 @@
+<tool id="cshl_fasta_nucleotides_changer" version="1.0.1" name="RNA/DNA" >
+    <description>converter</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fasta_nucleotide_changer
+-$mode
+-v
+-o '$output'
+    ]]></command>
+    <inputs>
+        <expand macro="fasta_input" />
+
+        <param name="mode" type="select" label="Convert">
+            <option value="d">RNA to DNA (U to T)</option>
+            <option value="r">DNA to RNA (T to U)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fasta_nuc_changer1.fasta" />
+            <param name="mode" value="r" />
+            <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
+        </test>
+        <test>
+            <param name="input" value="fasta_nuc_changer2.fasta" />
+            <param name="mode" value="d" />
+            <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool converts RNA FASTA files to DNA (and vice-versa).
+
+In **RNA-to-DNA** mode, U's are changed into T's.
+
+In **DNA-to-RNA** mode, T's are changed into U's.
+
+--------
+
+**Example**
+
+Input RNA FASTA file ( from Sanger's mirBase )::
+
+    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+    UGAGGUAGUAGGUUGUAUAGUU
+    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+    UCCCUGAGACCUCAAGUGUGA
+    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+    UGGAAUGUAAAGAAGUAUGUA
+
+Output DNA FASTA file (with RNA-to-DNA mode)::
+
+    >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+    TGAGGTAGTAGGTTGTATAGTT
+    >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+    TCCCTGAGACCTCAAGTGTGA
+    >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+    TGGAATGTAAAGAAGTATGTA
+
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out
new file mode 100644
index 00000000000..e46135f36f4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change1.out
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+UGAGGUAGUAGGUUGUAUAGUU
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+UCCCUGAGACCUCAAGUGUGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+UGGAAUGUAAAGAAGUAUGUA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+UAUCACAGCCAGCUUUGAUGUGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGUGUGGUUAGCUGGUUG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+UCACCGGGUGGAAACUAGCAGU
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+UCACCGGGUGAAAAUUCGCAUG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+UCACCGGGUGAACACUUGCAGU
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+UCACCGGGAGAAAAACUGGAGU
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+UCACCGGGUGUAAAUCAGCUUG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+UCACCGGGUGUACAUCAGCUAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+UCACCGGGUGAAAAAUCACCUA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+UCACCGGGUUAACAUCUACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+UAUCACAGUUUACUUGCUGUCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+UGACUAGAGACACAUUCAGCU
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+UGACUAGAGACACAUUCAGCU
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+UGUCAUGGAGUCGCUCUCUUCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+UGUCAUGGAGGCGCUCUCUUCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+UGAGGUAGGCUCAGUAGAUGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCUGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+UGAUAUGUCUGGUAUUCUUGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+UACCCGUAGCUCCUAUCCAUGUU
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGUACAUAUGUUUCCGUGCU
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGUACAUUUGUUUCCGUGCU
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+UACCCGUAAUCUUCAUAAUCCGAG
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out
new file mode 100644
index 00000000000..c42d9dc113f
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_change2.out
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+TGAGGTAGTAGGTTGTATAGTT
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+TCCCTGAGACCTCAAGTGTGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+TGGAATGTAAAGAAGTATGTA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+TATCACAGCCAGCTTTGATGTGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGTGTGGTTAGCTGGTTG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+TCACCGGGTGGAAACTAGCAGT
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+TCACCGGGTGAAAATTCGCATG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+TCACCGGGTGAACACTTGCAGT
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+TCACCGGGAGAAAAACTGGAGT
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+TCACCGGGTGTAAATCAGCTTG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+TCACCGGGTGTACATCAGCTAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+TCACCGGGTGAAAAATCACCTA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+TCACCGGGTTAACATCTACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+TATCACAGTTTACTTGCTGTCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+TGACTAGAGACACATTCAGCT
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+TGACTAGAGACACATTCAGCT
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+TGTCATGGAGTCGCTCTCTTCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+TGTCATGGAGGCGCTCTCTTCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+TGAGGTAGGCTCAGTAGATGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCTGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+TGATATGTCTGGTATTCTTGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+TACCCGTAGCTCCTATCCATGTT
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGTACATATGTTTCCGTGCT
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGTACATTTGTTTCCGTGCT
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+TACCCGTAATCTTCATAATCCGAG
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta
new file mode 100644
index 00000000000..c42d9dc113f
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer1.fasta
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+TGAGGTAGTAGGTTGTATAGTT
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+TCCCTGAGACCTCAAGTGTGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+TGGAATGTAAAGAAGTATGTA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+TATCACAGCCAGCTTTGATGTGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGTGTGGTTAGCTGGTTG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+TCACCGGGTGGAAACTAGCAGT
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+TCACCGGGTGAAAATTCGCATG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+TCACCGGGTGAACACTTGCAGT
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+TCACCGGGAGAAAAACTGGAGT
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+TCACCGGGTGTAAATCAGCTTG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+TCACCGGGTGTACATCAGCTAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+TCACCGGGTGAAAAATCACCTA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+TCACCGGGTTAACATCTACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+TATCACAGTTTACTTGCTGTCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+TGACTAGAGACACATTCAGCT
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+TGACTAGAGACACATTCAGCT
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+TGTCATGGAGTCGCTCTCTTCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+TGTCATGGAGGCGCTCTCTTCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+TGAGGTAGGCTCAGTAGATGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCTGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+TGATATGTCTGGTATTCTTGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+TACCCGTAGCTCCTATCCATGTT
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGTACATATGTTTCCGTGCT
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGTACATTTGTTTCCGTGCT
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+TACCCGTAATCTTCATAATCCGAG
diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta
new file mode 100644
index 00000000000..e46135f36f4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/test-data/fasta_nuc_changer2.fasta
@@ -0,0 +1,50 @@
+>cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
+UGAGGUAGUAGGUUGUAUAGUU
+>cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
+UCCCUGAGACCUCAAGUGUGA
+>cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
+UGGAAUGUAAAGAAGUAUGUA
+>cel-miR-2 MIMAT0000004 Caenorhabditis elegans miR-2
+UAUCACAGCCAGCUUUGAUGUGC
+>cel-miR-34 MIMAT0000005 Caenorhabditis elegans miR-34
+AGGCAGUGUGGUUAGCUGGUUG
+>cel-miR-35 MIMAT0000006 Caenorhabditis elegans miR-35
+UCACCGGGUGGAAACUAGCAGU
+>cel-miR-36 MIMAT0000007 Caenorhabditis elegans miR-36
+UCACCGGGUGAAAAUUCGCAUG
+>cel-miR-37 MIMAT0000008 Caenorhabditis elegans miR-37
+UCACCGGGUGAACACUUGCAGU
+>cel-miR-38 MIMAT0000009 Caenorhabditis elegans miR-38
+UCACCGGGAGAAAAACUGGAGU
+>cel-miR-39 MIMAT0000010 Caenorhabditis elegans miR-39
+UCACCGGGUGUAAAUCAGCUUG
+>cel-miR-40 MIMAT0000011 Caenorhabditis elegans miR-40
+UCACCGGGUGUACAUCAGCUAA
+>cel-miR-41 MIMAT0000012 Caenorhabditis elegans miR-41
+UCACCGGGUGAAAAAUCACCUA
+>cel-miR-42 MIMAT0000013 Caenorhabditis elegans miR-42
+UCACCGGGUUAACAUCUACAGA
+>cel-miR-43 MIMAT0000014 Caenorhabditis elegans miR-43
+UAUCACAGUUUACUUGCUGUCGC
+>cel-miR-44 MIMAT0000015 Caenorhabditis elegans miR-44
+UGACUAGAGACACAUUCAGCU
+>cel-miR-45 MIMAT0000016 Caenorhabditis elegans miR-45
+UGACUAGAGACACAUUCAGCU
+>cel-miR-46 MIMAT0000017 Caenorhabditis elegans miR-46
+UGUCAUGGAGUCGCUCUCUUCA
+>cel-miR-47 MIMAT0000018 Caenorhabditis elegans miR-47
+UGUCAUGGAGGCGCUCUCUUCA
+>cel-miR-48 MIMAT0000019 Caenorhabditis elegans miR-48
+UGAGGUAGGCUCAGUAGAUGCGA
+>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
+AAGCACCACGAGAAGCUGCAGA
+>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
+UGAUAUGUCUGGUAUUCUUGGG
+>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
+UACCCGUAGCUCCUAUCCAUGUU
+>cel-miR-52 MIMAT0000023 Caenorhabditis elegans miR-52
+CACCCGUACAUAUGUUUCCGUGCU
+>cel-miR-53 MIMAT0000024 Caenorhabditis elegans miR-53
+CACCCGUACAUUUGUUUCCGUGCU
+>cel-miR-54 MIMAT0000025 Caenorhabditis elegans miR-54
+UACCCGUAAUCUUCAUAAUCCGAG
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml
new file mode 100644
index 00000000000..f99db138e20
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/.shed.yml
@@ -0,0 +1,12 @@
+categories:
+- Fastq Manipulation
+- Graphics
+- Statistics
+description: Draw quality score boxplot
+long_description: |
+  Creates a boxplot graph for the quality scores in the library.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fastq_quality_boxplot
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml
new file mode 100644
index 00000000000..9e856f28042
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml
@@ -0,0 +1,68 @@
+<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
+fastq_quality_boxplot_graph.sh
+-t '$escaped_element_identifier'
+-i '$input'
+-o '$output'
+    ]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="txt" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="png" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastq_quality_boxplot-in1.fastq" />
+            <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="768" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Creates a boxplot graph for the quality scores in the library.
+
+.. class:: infomark
+
+**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
+
+-----
+
+**Output Examples**
+
+* Black horizontal lines are medians
+* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
+* Whiskers show outlier at max. 1.5*IQR
+
+
+An excellent quality library (median quality is 40 for almost all 36 cycles):
+
+.. image:: fastq_quality_boxplot_1.png
+
+
+A relatively good quality library (median quality degrades towards later cycles):
+
+.. image:: fastq_quality_boxplot_2.png
+
+A low quality library (median drops quickly):
+
+.. image:: fastq_quality_boxplot_3.png
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png
new file mode 100644
index 00000000000..f721716a18c
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_1.png differ
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_2.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_2.png
new file mode 100644
index 00000000000..0ce5baf5fda
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_2.png differ
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_3.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_3.png
new file mode 100644
index 00000000000..e21c49be929
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot_3.png differ
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq
new file mode 100644
index 00000000000..852c8122efe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-in1.fastq
@@ -0,0 +1,37 @@
+column	count	min	max	sum	mean	Q1	med	Q3	IQR	lW	rW	A_Count	C_Count	G_Count	T_Count	N_Count	Max_count
+1	9	23	34	288	32.00	33	33	33	0	33	33	3	1	4	1	0	9
+2	9	28	33	287	31.89	31	33	33	2	28	33	3	3	2	1	0	9
+3	9	13	34	268	29.78	28	33	33	5	21	34	5	1	0	3	0	9
+4	9	17	33	261	29.00	30	33	33	3	26	33	1	2	3	3	0	9
+5	9	22	33	269	29.89	30	33	33	3	26	33	3	3	3	0	0	9
+6	9	22	33	277	30.78	30	33	33	3	26	33	5	3	0	1	0	9
+7	9	21	33	258	28.67	24	33	33	9	21	33	4	1	3	1	0	9
+8	9	12	33	263	29.22	32	33	33	1	31	33	2	1	1	5	0	9
+9	9	29	33	290	32.22	33	33	33	0	33	33	3	3	2	1	0	9
+10	9	23	33	277	30.78	32	33	33	1	31	33	1	4	2	2	0	9
+11	9	12	33	245	27.22	21	31	33	12	12	33	5	2	1	1	0	9
+12	9	13	33	214	23.78	15	24	33	18	13	33	2	4	2	1	0	9
+13	9	5	33	249	27.67	29	31	33	4	23	33	2	1	1	5	0	9
+14	9	5	33	233	25.89	24	33	33	9	11	33	3	3	2	1	0	9
+15	9	15	33	251	27.89	24	33	33	9	15	33	5	1	1	2	0	9
+16	9	23	34	269	29.89	24	33	33	9	23	34	3	1	2	3	0	9
+17	9	13	34	266	29.56	33	33	33	0	33	33	2	3	1	3	0	9
+18	9	21	34	272	30.22	31	33	33	2	28	34	0	5	1	3	0	9
+19	9	5	34	244	27.11	27	30	33	6	18	34	4	4	1	0	0	9
+20	9	11	34	241	26.78	23	32	33	10	11	34	3	4	2	0	0	9
+21	9	13	33	240	26.67	24	27	33	9	13	33	1	4	0	4	0	9
+22	9	5	33	190	21.11	13	21	33	20	5	33	1	4	0	3	1	9
+23	9	5	33	205	22.78	16	26	33	17	5	33	4	4	1	0	0	9
+24	9	5	33	247	27.44	28	31	33	5	21	33	1	5	1	2	0	9
+25	9	11	34	241	26.78	24	33	33	9	11	34	3	4	0	2	0	9
+26	9	5	33	212	23.56	18	31	33	15	5	33	0	6	0	3	0	9
+27	9	5	33	227	25.22	21	26	33	12	5	33	3	4	1	1	0	9
+28	9	21	33	255	28.33	24	31	33	9	21	33	2	4	3	0	0	9
+29	9	5	33	228	25.33	21	30	33	12	5	33	2	4	1	2	0	9
+30	9	10	33	213	23.67	16	28	33	17	10	33	3	4	2	0	0	9
+31	9	5	33	236	26.22	21	31	33	12	5	33	1	4	1	3	0	9
+32	9	5	33	210	23.33	12	29	33	21	5	33	3	3	0	3	0	9
+33	9	5	33	183	20.33	9	21	33	24	5	33	1	4	2	2	0	9
+34	9	5	33	150	16.67	7	17	22	15	5	33	3	4	1	1	0	9
+35	9	13	33	217	24.11	21	24	29	8	13	33	1	4	1	3	0	9
+36	9	5	33	195	21.67	18	21	32	14	5	33	3	2	1	3	0	9
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-out1.png b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-out1.png
new file mode 100644
index 00000000000..afeff9d3b80
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_quality_boxplot-out1.png differ
diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out
new file mode 100644
index 00000000000..852c8122efe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out
@@ -0,0 +1,37 @@
+column	count	min	max	sum	mean	Q1	med	Q3	IQR	lW	rW	A_Count	C_Count	G_Count	T_Count	N_Count	Max_count
+1	9	23	34	288	32.00	33	33	33	0	33	33	3	1	4	1	0	9
+2	9	28	33	287	31.89	31	33	33	2	28	33	3	3	2	1	0	9
+3	9	13	34	268	29.78	28	33	33	5	21	34	5	1	0	3	0	9
+4	9	17	33	261	29.00	30	33	33	3	26	33	1	2	3	3	0	9
+5	9	22	33	269	29.89	30	33	33	3	26	33	3	3	3	0	0	9
+6	9	22	33	277	30.78	30	33	33	3	26	33	5	3	0	1	0	9
+7	9	21	33	258	28.67	24	33	33	9	21	33	4	1	3	1	0	9
+8	9	12	33	263	29.22	32	33	33	1	31	33	2	1	1	5	0	9
+9	9	29	33	290	32.22	33	33	33	0	33	33	3	3	2	1	0	9
+10	9	23	33	277	30.78	32	33	33	1	31	33	1	4	2	2	0	9
+11	9	12	33	245	27.22	21	31	33	12	12	33	5	2	1	1	0	9
+12	9	13	33	214	23.78	15	24	33	18	13	33	2	4	2	1	0	9
+13	9	5	33	249	27.67	29	31	33	4	23	33	2	1	1	5	0	9
+14	9	5	33	233	25.89	24	33	33	9	11	33	3	3	2	1	0	9
+15	9	15	33	251	27.89	24	33	33	9	15	33	5	1	1	2	0	9
+16	9	23	34	269	29.89	24	33	33	9	23	34	3	1	2	3	0	9
+17	9	13	34	266	29.56	33	33	33	0	33	33	2	3	1	3	0	9
+18	9	21	34	272	30.22	31	33	33	2	28	34	0	5	1	3	0	9
+19	9	5	34	244	27.11	27	30	33	6	18	34	4	4	1	0	0	9
+20	9	11	34	241	26.78	23	32	33	10	11	34	3	4	2	0	0	9
+21	9	13	33	240	26.67	24	27	33	9	13	33	1	4	0	4	0	9
+22	9	5	33	190	21.11	13	21	33	20	5	33	1	4	0	3	1	9
+23	9	5	33	205	22.78	16	26	33	17	5	33	4	4	1	0	0	9
+24	9	5	33	247	27.44	28	31	33	5	21	33	1	5	1	2	0	9
+25	9	11	34	241	26.78	24	33	33	9	11	34	3	4	0	2	0	9
+26	9	5	33	212	23.56	18	31	33	15	5	33	0	6	0	3	0	9
+27	9	5	33	227	25.22	21	26	33	12	5	33	3	4	1	1	0	9
+28	9	21	33	255	28.33	24	31	33	9	21	33	2	4	3	0	0	9
+29	9	5	33	228	25.33	21	30	33	12	5	33	2	4	1	2	0	9
+30	9	10	33	213	23.67	16	28	33	17	10	33	3	4	2	0	0	9
+31	9	5	33	236	26.22	21	31	33	12	5	33	1	4	1	3	0	9
+32	9	5	33	210	23.33	12	29	33	21	5	33	3	3	0	3	0	9
+33	9	5	33	183	20.33	9	21	33	24	5	33	1	4	2	2	0	9
+34	9	5	33	150	16.67	7	17	22	15	5	33	3	4	1	1	0	9
+35	9	13	33	217	24.11	21	24	29	8	13	33	1	4	1	3	0	9
+36	9	5	33	195	21.67	18	21	32	14	5	33	3	2	1	3	0	9
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml
new file mode 100644
index 00000000000..791bccfe3c9
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/.shed.yml
@@ -0,0 +1,10 @@
+categories:
+- Fastq Manipulation
+description: Quality format converter (ASCII-Numeric)
+long_description: |
+  Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fastq_quality_converter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml
new file mode 100644
index 00000000000..dbfcceedd42
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml
@@ -0,0 +1,104 @@
+<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.1">
+    <description>(ASCII-Numeric)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastq_quality_converter
+$QUAL_FORMAT
+-o '$output'
+@FQQUAL@
+    ]]></command>
+    <inputs>
+        <expand macro="fastq_input" />
+
+        <param name="QUAL_FORMAT" type="select" label="Desired output format">
+            <option value="-a">ASCII (letters) quality scores</option>
+            <option value="-n">Numeric quality scores</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="fastq" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- ASCII to NUMERIC -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <output name="output" file="fastq_qual_conv1.out" />
+        </test>
+        <test>
+            <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <output name="output" file="fastq_qual_conv1a.out" />
+        </test>
+        <test>
+            <!-- NUMERIC to ASCII -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <output name="output" file="fastq_qual_conv2.out" />
+        </test>
+        <test>
+            <!-- NUMERIC to NUMERIC (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <output name="output" file="fastq_qual_conv2n.out" />
+        </test>
+        <test>
+            <!-- ASCII to NUMERIC -->
+            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in5.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <output name="output" file="fastq_quality_converter-out5.fastq" />
+        </test>
+        <test>
+            <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in6.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <output name="output" file="fastq_quality_converter-out6.fastq" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
+
+.. class:: warningmark
+
+Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
+
+-----
+
+FASTQ with Numeric quality scores::
+
+    @CSHL__2_FC042AGWWWXX:8:1:120:202
+    ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+    +CSHL__2_FC042AGWWWXX:8:1:120:202
+    40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
+    @CSHL__2_FC042AGWWWXX:8:1:103:1185
+    ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
+    +CSHL__2_FC042AGWWWXX:8:1:103:1185
+    40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
+
+
+FASTQ with ASCII quality scores::
+
+    @CSHL__2_FC042AGWWWXX:8:1:120:202
+    ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+    +CSHL__2_FC042AGWWWXX:8:1:120:202
+    hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
+    @CSHL__2_FC042AGWWWXX:8:1:103:1185
+    ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
+    +CSHL__2_FC042AGWWWXX:8:1:103:1185
+    hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq
new file mode 100644
index 00000000000..76c0d6c4f2a
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out
new file mode 100644
index 00000000000..73283203055
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1.out
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+33 33 34 30 22 30 33 21 29 32 33 33 30 33 26 33 33 33 34 34 24 5 26 33 34 33 33 33 33 33 33 33 33 29 29 32
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+23 33 33 33 30 33 26 33 33 23 30 21 31 24 33 23 33 33 28 23 13 5 16 30 11 5 26 24 18 16 5 5 5 7 33 33
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+33 31 13 30 33 28 21 33 33 33 31 13 31 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 22 28 26 21 7 21 21 18
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+33 30 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 31 21 32 33 33 33 33 33 31 19 31 33 33 33 33 33 22 22 27
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+34 33 34 33 33 33 33 33 33 33 21 13 33 33 33 33 33 33 33 33 33 33 33 28 24 5 21 21 5 16 31 29 21 5 18 5
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+33 28 28 17 22 22 22 12 33 33 12 15 5 24 21 23 21 21 5 11 21 21 12 5 13 21 5 21 21 11 21 12 9 17 13 21
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+33 33 33 33 33 33 33 33 33 24 21 24 24 5 24 33 33 33 33 33 32 31 26 33 33 33 33 33 33 33 33 33 24 5 24 21
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+33 33 27 19 30 32 24 32 33 33 31 29 29 15 15 24 13 21 30 31 27 13 21 31 33 33 33 33 33 33 33 33 33 33 33 33
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+33 33 33 33 33 33 33 33 30 33 33 33 33 33 33 34 34 34 27 11 24 16 5 21 27 18 24 26 30 10 21 11 18 11 24 5
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out
new file mode 100644
index 00000000000..76c0d6c4f2a
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv1a.out
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCCCCATGTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCTACTCATCCCAGTAGAGGCCCGTGGCC
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACACACACTCATCGTCGTCCCCCG
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACCC
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGGCGCTGTGGAGAGTGTCACACCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGACGCGGCCGCTCGCGCTCT
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq
new file mode 100644
index 00000000000..e3caaf2d9f2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.fastq
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out
new file mode 100644
index 00000000000..56cb36d4af0
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2.out
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+hhhhhhhhhhhhhhhhhh`hhhhPTYIUehhP]Z^
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+hhhhhhhhhhhhhhhhhhhhhhh;MQ\hhHQ[HMJ
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+hhhhhhhhhhhhhhhDhhZchfhFhh@CZ`[NKZK
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+hhhhhhhhhhhhchhLhh^^hhhLdWQXRVYOJbN
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+hhhhhhhhhhhhhhhhhPW\hUhIeMTUGKNNFWJ
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+hhhhhhhhhhhhhhhhhhhhh`hLfOVTQNLJGVK
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+hhhhhhhhhhhhhhYhhhhhhh_hhKJWhMLQeQV
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+hhhhhhhhhhhhhhhhhhgV_hhL]V@GLHRGCRI
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+hhghhhhhhhhhDhhXbTaUd`h;hMUUZQRYNYU
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+hhhhhhhhhhhhhchhhhhahehhhRPTWV_ZJVS
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+hhhhhhhhhhhhhY[hec[hhQh;dKSOSPKLLWK
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+hhhhhhhhhhhhhhhhhhhhhh^hhXRfaZPWVPR
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+hhhhhhhhchghh[ThQbOhhhhO\QDLJJRNCNK
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+hhhhhhhhhhhhhhd`hahhfeh\][VMTSQQMaR
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+hhhhhhhhhhhahhhhhXhhhhhLhXNIVO]RKhV
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out
new file mode 100644
index 00000000000..e3caaf2d9f2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_qual_conv2n.out
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq
new file mode 100644
index 00000000000..379f94e2911
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in5.fastq
@@ -0,0 +1,2000 @@
+@chr1_177668195_177668687_1:0:0_2:0:0_0/1
+CCCTTGCCTTCCTAGCTTTCAGTATTACCCACTAAGAACACATAAACATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_102240227_102240757_1:0:0_0:0:0_1/1
+AATGGATGCAGAAAATGTGGTACATCTACACAATGGAATCCTACTCAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_135092709_135093083_1:0:0_0:0:0_2/1
+GATCTTGACATAAAGCAAAGGTTGTTAAACCAAGGCCTGCTTGCCCTGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173363751_173364238_0:0:0_1:0:0_3/1
+GAGGGCAGAGAGAAAATCTAAAGTGCAGTCTACTGGTCCTCAGTGGAGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_155990043_155990565_1:0:0_0:0:0_4/1
+AAGCTTGCCGGTCTTCTGTGGGGCAGAGAACCCAGCTGCTCTTTTTCTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_3703883_3704401_0:0:0_1:0:0_5/1
+CTCTTGCAGGAATGAAGCCTTAACGAAAATAGACTGGTAGTGACAATATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_148211558_148212105_1:0:0_2:0:0_6/1
+AATTTCTTTAGTGATAATTAGTTTCTTGTATACTTTGCCCTCCTAACCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_30961675_30962138_2:0:0_0:0:0_7/1
+AAAAACAGGAAAACACATCCAAACAGGTAATGGAAATGAACAAAACCATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86070681_86071151_1:0:0_0:0:0_8/1
+GAGCCACTTGCAGAACATTCTAATTGTTTCCAACTTTAAGAATAATTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78259267_78259767_0:0:0_1:0:0_9/1
+TACCTTCACATCCCCCTCTACTTCTTTCCACCCCCGGTCACTGGGATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_143451378_143451824_2:0:0_1:0:0_a/1
+TCTTTTTGTCTTATAGACGGTGTCTTTTGCCTTGCAGAAACTTTGGAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_163539961_163540475_1:0:0_1:0:0_b/1
+GGCACACCTGTGATCCTGATCTTGAGGCTGGGAGATACAAGTTTCTGACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_70390520_70391012_0:0:0_1:0:0_c/1
+TCAGTTCAACATGTAGAAATCCCTTATGAATAATCTTGTCACTGTCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_119090463_119090959_0:0:0_0:0:0_d/1
+GATGATGATGATGATGCCCAAGATGATGATGATATAGCATGCCTAAAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_12587911_12588392_1:0:0_2:0:0_e/1
+AGAAACGGCTAGCACATGATTAGTATCCTGTCCTCTCCCATGAGTCTGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_21875665_21876102_0:0:0_1:0:0_f/1
+GCTAAAAGCAGTAAAGAATGAGAACACAGAGTGTTTAATGATATTACGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_22900274_22900767_0:0:0_0:0:0_10/1
+TTCTTTTTTTTTCTTAGAAAATCAGTGTTTACTTATTACTTTTATTAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_97511239_97511754_1:0:0_0:0:0_11/1
+AGAATTTTGGGTCCTGTTTGTGTAGCCAGTCTTTTAGTCTATGTCTTCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_64669865_64670428_2:0:0_2:0:0_12/1
+ACTCACATGATTGAGTTTCTAAAATCCTTACCAGTAATTCCCCCTGGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_69102786_69103213_3:0:0_1:0:0_13/1
+TTTTCAAAATAGCAAAAACTTTTTTTATTTTTTTGGTGTTCTGCTGCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117742994_117743506_1:0:0_4:0:0_14/1
+CCGGGATCAAGCTCAAGGAGATTGTCCTTGGACCTGACACTATTACTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53703453_53703930_0:0:0_1:0:0_15/1
+CGTCACAACATACTGAGCACCAGGAGCAAGTACTGCGGATCTGTGGGACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_17968135_17968661_2:0:0_0:0:0_16/1
+ATCAATAGTACTGTGAAAGCAAATGCTGGTGAGGATGTGAACAAAGGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126734590_126735074_2:0:0_1:0:0_17/1
+AAGGTCCCCCATACCCACCCCCCAATCCCCTAGCCACCCACTCCCCCTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_15473022_15473574_0:0:0_2:0:0_18/1
+GGGCTCTTCTCTTTGGTGTCATCCTCTGAAGTAGGAACCAGTTCATTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_32809503_32810008_3:0:0_4:0:0_19/1
+ACACGTGGTGTTCAGTGTCACCCCATGTAGATGGGGATGTTCCCTAGGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_101160086_101160574_0:0:0_2:0:0_1a/1
+TGTGTGTACGACTGTTTCTGTGAAGGTAAACAAGAGGAGGTTGCACATGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_86845143_86845638_2:0:0_0:0:0_1b/1
+AGCCTTAATTAGTAGGGCTTGGTTTTTTTTGGGGGGGTGGGCTTGGGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_156394447_156394901_0:1:0_1:0:0_1c/1
+TAGGGAACTTTTGGGACAGCATTTGAACTGTAAATAAAGAAAATATCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_175220096_175220545_0:0:0_1:0:0_1d/1
+GTCAGCATATTCAATCACACTTTACCTCTTCCCTGCCTCACTTCAGTGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_66136304_66136892_1:0:0_0:0:0_1e/1
+CCTTATCACCATCTTTGACCTCTCTTTCCACTGACTGGAACCCCATTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_56699450_56700040_1:0:0_0:0:0_1f/1
+GTTCAACTCCTGTCTCCCCCACTGCCCCCCCCCCAGCTCAGCCACCTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_60449644_60450153_0:0:0_0:0:0_20/1
+TAGCACCTGTATACAAAAGTCACGTAATGTGGTATGCATGTTTGTTTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_28286517_28287074_0:0:0_0:0:0_21/1
+ATTTTGATTTTCATTTTTTTTCCTGCTTTGAAGTATTGTATAGAGGAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_127946423_127946897_1:0:0_1:0:0_22/1
+CATTTAATTCCAGCACTCCAGATGCAGAAGCAGGCAGTTTGAGGTCAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_136274524_136275031_0:0:0_3:0:0_23/1
+TAGATTGTGCTTTGATTCAGAGTAAAGAAAAGAGGACATGGCAAAAGCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_122372156_122372666_1:0:0_1:0:0_24/1
+TTGTGTGTGCTCATGTACAAACACACACACACACACTGAAGTTAAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_19553027_19553520_1:0:0_0:0:0_25/1
+AGATCAAAGATCTGTGAAGAGGGGAACCATGAATACAAATGGTAGAAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_57071218_57071658_1:0:0_0:0:0_26/1
+CCCTGAGGCATGTGGGCAGCCCTATGTGGACTCCATAGTTGACAAGAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_7557012_7557560_0:0:0_2:1:0_27/1
+TGGCTAAGCCCAACTCCTTACTTACAATTTAGTTATTTGAGCTTCTCTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_18791508_18791966_0:0:0_0:0:0_28/1
+GCATTGGTTGAAAAGCATGAAAGTTCTATGAGGAAAAAAAAAATAGAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_56244256_56244708_0:0:0_0:0:0_29/1
+TCCTTATTGGATTTTATTAAAAACAAAAATGATTATCATGTTTATTTTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_30613322_30613773_2:0:0_1:0:0_2a/1
+GACAGTTTCTATGAACCTCAAACAATAGCACATTTGCATAGCGGGTTCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_161898116_161898586_1:0:0_1:0:0_2b/1
+GTTGATGCTGAGTTATGAGTCCAAATGATGAATGTTGCACTTGAACAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_3742828_3743343_1:0:0_0:0:0_2c/1
+ATAGATGACATAGATACATGATACATGATGTATGATATATACTATATGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_59624032_59624611_1:0:0_0:0:0_2d/1
+ACCTTAGCCATCTAGTTTTTTTGTGATTGTTGTTTGATTTTTGAGATGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_98734890_98735381_1:0:0_2:0:0_2e/1
+AATTGTGACATAGCAGTAACTCTTGTGTCTTAAGTGTGTTGTATCACATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_170863521_170863976_0:0:0_1:0:0_2f/1
+CAGAAACGTCCACTCACTGCTGATGGAGACACAGAACTGCAAGTTTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_111611961_111612483_3:0:0_0:0:0_30/1
+TCTTTTTTTATTTTAATATTTATTTATTATTATTAAGTCTAAGTACACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_125730124_125730581_1:0:0_1:1:0_31/1
+ATTGAAGGGCAATTCCCTTTGCCCTTTATTGCCTCTGCAGGCCATGTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_10873266_10873801_1:0:0_1:0:0_32/1
+TATAAAGGCAGAGTCTCTCTTTTAACATAAAGCTTTGTCTAGTCAGCTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_175631956_175632547_3:0:0_1:0:0_33/1
+TTTAAGAGAGACTGATGAGATGTGGGAGACGGAAGAGTGTGGAAGGGTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_20372115_20372592_0:0:0_2:0:0_34/1
+TCCTCACTTAAACTATTAGAAGGTAGTCAAATTTTTTTGGAAGAGTATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_172022589_172023145_0:0:0_2:0:0_35/1
+TACATCATAGTATATGTCATGCTTTTTATGGCTAAGTAATATTCTACTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_168140019_168140474_0:0:0_1:0:0_36/1
+AGAGAGAAAGTGGCAGGGGGTAGACCTGCAGGCCAGGAACATCAAAGGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_12207936_12208461_1:0:0_0:0:0_37/1
+GAATCAAAAAAGAAACTGACATCACAAAAATTCAAAAAAATGTATTGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73438005_73438553_2:0:0_0:0:0_38/1
+TTATCATGTTCTTCTCAGGTCCCTCCCCTCTGGCCTCTATCATCCTCCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_152770828_152771350_1:0:0_1:0:0_39/1
+TGGAACAGAATATTTAGACATGTGTATGCTGGGCACAAACCCTTAGGAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_23377131_23377643_1:0:0_1:0:0_3a/1
+TGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGTTAGCTCGGGGGTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_101774130_101774651_1:0:0_0:0:0_3b/1
+ACCAAAACCAAAACCAAAAACAAACACCTCTGTAATAATCTGTATCTGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44505664_44506178_2:0:0_1:0:0_3c/1
+GTAGAATCACCTGAATATTGAGTTAGGTGATAGAAGAACGAGTTAAAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_136585250_136585783_0:0:0_0:0:0_3d/1
+ACAAGCTGTACCTTAGGACCCCCATGCATTGGCAGTGATTGTGAATAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_125479421_125479942_1:0:0_1:0:0_3e/1
+CAGTTAGTGATCAACCTCCTGCTGATCAAATTTCCTTGAATGTATGCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_48288718_48289238_0:0:0_2:0:0_3f/1
+GCTGAGAAGAATGTATACCCTTTTGATTTAGGATAAAATGTTCTGTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_162596088_162596584_0:0:0_1:0:0_40/1
+ATGTTTTATAATTAATGTTTTAAAATTAACTTTACAATACTATGTTTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_114964476_114965085_0:0:0_0:0:0_41/1
+AAAAATACATTATGGTTTGCAAAGAATATTTAATAATGTTTCTAAAACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_132214583_132215104_0:0:0_1:0:0_42/1
+GAAGGAGAAGGAGAAGGAAAGAAGAAGAAGAAAGTCATCCAGGTCAGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_4422836_4423410_1:0:0_1:0:0_43/1
+TGTAAAGTAGCATAGAACTTGCTTTCTTGTTTTATAGAGATTCTTCGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72831428_72831958_1:0:0_0:0:0_44/1
+TTGACAAAAGCAACTGAAGGAAGGCAGAGATTATTTTGGCCCTCAGCACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17626572_17627059_2:0:0_0:0:0_45/1
+TCACACATGAATGCACTCACATATGCACACGTATTTTAAATATAATTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_122621502_122622050_0:0:0_1:0:0_46/1
+CTAAATGTCTTTTATAGTCATTTATTTGGGACTAATCAGATGGATTAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157981625_157982140_2:0:0_1:0:0_47/1
+AGGGAATTACCGGTTCAGAATTCAAACTTCAAAAGACAGATAAACATTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86952334_86952916_0:0:0_1:0:0_48/1
+TCTGCAAGTACTCAGCGAAGCTGCCCACACAGGACTTTTCGTCATGTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_56589802_56590323_0:0:0_5:0:0_49/1
+GTCGTGAAGTGACCGACAGTATATATGGCTAAATATATATATATATATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44959275_44959852_2:0:0_0:0:0_4a/1
+CCCGCCGAACTTAGGAAATTAGTCTGACCAGGTGAGAGGTTGCGCCAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_78655270_78655764_0:0:0_1:0:0_4b/1
+GCACAAGGGACTGCCTACTCCTGTTCATGATTTCATGTGGTTGACCCTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_92742731_92743276_3:0:0_1:1:0_4c/1
+TGACCAGGCGGCTGGAGGTCAAGGGTCTGTCGTAAGAGAATCCCATTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133350357_133350894_2:0:0_0:0:0_4d/1
+TGGCCAAAAGGACTGGATGATCCAACGTATAGACAGCTGAGGGCGTTAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_18383798_18384307_2:0:0_0:0:0_4e/1
+CTTATTATCCTAATGCTACCAAATCACAAGGTTTGCTGTTTCTTCCTGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_94539200_94539737_1:0:0_1:0:0_4f/1
+CAGTGTTGTTTTTATTTGCATTTCCCTGATGATTAAGGATGTTGAACATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_131360576_131361118_1:1:0_0:0:0_50/1
+CAGGGTGACACAGTGAAACCTTCTCTTAAACAGTTTCCTAGGACATATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_55802170_55802665_0:0:0_1:0:0_51/1
+AATGATATAAAACCATTTGAACTGTTCCTCTTTCGCCCACAACACACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_160986523_160987031_0:0:0_1:0:0_52/1
+AGCAACAGAGCAACCTTGCAATGGTGGTCGCCAAGGAAACAGCATCATCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_10207724_10208191_1:0:0_1:0:0_53/1
+TCAAGCATCATTCCTTGGGTACAACCCATTTTATTTTTAAATAGGGACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_186877031_186877586_1:0:0_0:0:0_54/1
+TGTGGAACCTATAGGAGCCTTTTCTCAGTCAGTACCACACAGGTGATGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_76761957_76762468_0:0:0_4:0:0_55/1
+ACAAGAGAAAGCTATATCTGGGTCCTTTCAGCGAAATCTTGCTAGTGTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117599116_117599626_3:0:0_1:0:0_56/1
+TGGATGGTTCATTCCTATTTAAAAGAGGGAAACAAATAGTCACTGGAGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_174656805_174657230_0:0:0_2:0:0_57/1
+GCTTATGTTGCTAATGGCCTTGCATCTTCCTCTCAATAATATATGTTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_31215276_31215715_1:0:0_3:0:0_58/1
+GTGCCTTGTGACTGATTTGGTTTGAAATATTTTTAAGAATAAAATTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_126165616_126166084_1:0:0_0:0:0_59/1
+TTTTCTTACATCTGAACTTGGGCCAGAAAGCAGTTTAGTTTTCAAAGAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_164029809_164030262_1:0:0_2:0:0_5a/1
+TGTAGGCGGGATGAGCGGAATTCTACCCACACTTCAAATAACCAAAGCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_121717872_121718374_3:0:0_3:0:0_5b/1
+AGTTTGGGACAAGCAGAATAGACATGCAGTTTCCCTTTCCACCACTACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_160410719_160411215_0:0:0_1:0:0_5c/1
+TCTAATTTTTAAGAATGTGTTTATTTTGTGTTTGGGTATGGGATGCTAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100203985_100204499_0:0:0_1:0:0_5d/1
+GCAAAGAGTAAGATTGCCAACTCTAATTCCCATTTGGCTCCCATGGGCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177503365_177503816_3:0:0_0:0:0_5e/1
+TAGCTCGATCCAATCACAAACATTTCACGGACACACCAGCAGTCCAGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_164919242_164919704_1:0:0_1:0:0_5f/1
+CTTTGAAGGTCTGATAGAACTCTGCACTAAATCCATGTGGTCCTGGGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36958484_36958940_1:0:0_2:0:0_60/1
+TCTGGAGTTCCACGGGAAATAGACAGCAGCCTGTGTAACGGGGTCCTCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_99520185_99520697_2:0:0_2:0:0_61/1
+GGAGAGGGAGAGGGAGAGGTAGAGGGAGAGGGAGAGGGAGAGGGATAGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_92584393_92584910_1:0:0_1:0:0_62/1
+CCACTCACTCCCACTTCTTGGCCCTGGTGTTCCCCTTTACTGGGGCATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_6665937_6666494_1:0:0_2:0:0_63/1
+GAGGCACAGGTGGGCAGATCTCTGTGAGTTTGAGGCCAGCCTGAAATATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_103781308_103781731_2:0:0_0:0:0_64/1
+CCAATAGTTTTGTCATTGAACTTAAGGCCAACTTAATGGGAAGAAACTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_35981688_35982179_0:0:0_1:0:0_65/1
+TAATAAAGCTTTTTTATTCATGTACACAGGCTACCTCCATAAGGCAGGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_76873892_76874342_1:0:0_1:0:0_66/1
+GGTGTAAACCACCCACCCCTGCCCTTTGCCAGAAACCATCATGTTTATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148924276_148924708_1:0:0_0:0:0_67/1
+AACACAATGAGCTAGGGGCCCTCCCACATTGTTTCTAATTAAGGCAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_48352388_48352886_0:0:0_0:0:0_68/1
+TATTTTTCATCCTGAACCTTAATAATCAAGGTGGGGAAGAAACCCTGGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_135109139_135109668_0:0:0_0:0:0_69/1
+GACTAGGAAATAATGCTAGGCACTTGATTGGCCAGCCAGGCTAGAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_133271389_133271883_0:0:0_0:0:0_6a/1
+TGGTTTTTTGTTCTATTTTTTTTAAGATTTATTTTATTTATATGAGTACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_143528403_143528953_0:0:0_3:0:0_6b/1
+GAATCCATTGGCTTGATGTTTCTGGTAGCTGATAATCATTACACATGCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_60739061_60739616_3:0:0_1:0:0_6c/1
+GAAGCAAACTTCCCTAACCTAAAGAAATAGATTCCCACAAACATACAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86239673_86240187_2:0:0_0:0:0_6d/1
+GGTCCTTAGGAGACCCATGCAGTCCCCACTGTACATCGCCAGAAACAGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_8425683_8426176_2:0:0_1:0:0_6e/1
+GTTATTCATCTTGCCATTTTTGAAAATATTAATTATAAGTTTTCTGGTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_34934564_34935093_3:0:0_0:0:0_6f/1
+CCTTATAAAAAGTAGACATGCCATATAACTACATTTAGATCAGCAGTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_43897170_43897709_4:0:0_1:0:0_70/1
+TTGTGGGCATGTCCTCTGGACGAATGACAGGCTGTGGGCCTTTCGTACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_64512455_64512956_0:0:0_0:0:0_71/1
+ATTAGAAGGCACAGTATACATGGATGTACATACCCCATGAATAAATACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72637152_72637620_2:0:0_2:0:0_72/1
+TTTTTTTACAAGAAATAAAGCAGGTCGGTTGCTCTTGAGCATGGCAGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_149528405_149528902_2:0:0_0:0:0_73/1
+GCCACTGTTCCCATTGGTTGGGACCCACACGAAGGTCAATCTGCGCATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_89951120_89951611_2:0:0_1:0:0_74/1
+AGCCTAGCTGGCCCTAAGGGACAGCCCCTCCCATGGCTAGCCAGTCCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_108291981_108292457_1:0:0_1:0:0_75/1
+GAAAACTTCCCAAACATAAAGAAAGAGATGCGCATGATCATACAAGAAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130354891_130355474_0:1:0_0:0:0_76/1
+ATATCAAGCTCACTCTCTCTTGGCAATGTGCTGGGCACATTCATCACTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_166207187_166207634_1:0:0_3:1:0_77/1
+CAGAGAACCAGCTCAGCTTCTGGCACTCATGTCAGACAGCTTACAACCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_178111549_178112035_3:0:0_3:0:0_78/1
+GTTTTTGAAAAGTGGGTTTTGGGGAATCAACCTCACATCCATGTTCTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_64705135_64705653_1:0:0_3:0:0_79/1
+TGGGATTTGTTTTCTTTTTAGATTTTGCAGACTTGGGTTTATTACTGTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_50237028_50237524_0:0:0_2:0:0_7a/1
+TCATATCCAATATATATAAAGAACTCAAGAAGTTGGACTCTAGAAAACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_134752385_134752911_2:0:0_0:0:0_7b/1
+TTTCTGGGCCCAAGGTTTTCAGAAAGCAAATCAAATCCTTAGGTGAGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_168207741_168208312_2:0:0_0:0:0_7c/1
+CCTAGGTAGCCGGCAAATGTGAATGTAATAGAAAATTTAAATTTTAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_151034392_151034882_0:0:0_0:0:0_7d/1
+GGGGGTAGAACTTTTCCAAATTTTCCAAGAAACTGCCAAATTGATTTCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_149618965_149619431_0:0:0_1:0:0_7e/1
+TTTTTTTTTTTTTTTTTGGAGGGGGTGTTTTTAAAACCCATCAAAAAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72479618_72480144_1:1:0_0:0:0_7f/1
+TGTTCTCTTGAGAGCAAGCAACGTGACGGCTGGTTAGACGGCAGCCGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_18771436_18771929_1:0:0_2:0:0_80/1
+CTTTCGGGATGCAAACCCCTTCAGCTCCTTCAGTCCTTGCTCTAACTCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626454_177626877_2:0:0_1:0:0_81/1
+CCAATAGATGTCCATAGTGAAGCCCTCTGTCTCTCTGCACCTCTCTCATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_58671914_58672334_4:0:0_0:0:0_82/1
+GCAGCATTTGGGAGGCAGAGGCATGTGGATCTCTGTGCGATCAAGTACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_123634655_123635138_1:0:0_1:0:0_83/1
+TAGTAAGTTGTATTTTCACCACAGCATGAACCGTTGCTTACAGCATCACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32777949_32778514_0:0:0_2:0:0_84/1
+AGAACCATTACAATAGTTGAAAGGAGAAAATTTCAGTTAACTAGGGAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321026_38321532_2:0:0_2:0:0_85/1
+TTACATGTCTCCTAAATGAGCATACCAGAGTTCGGCCCAGAAGATGCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_31837668_31838221_1:0:0_2:0:0_86/1
+CCTAGAAAAAAGAACAGGCAACTAATAACTACTGAGAGAGGTAGAATTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_189752778_189753180_2:0:0_0:0:0_87/1
+AGGGTCCCACCTCAGGTGGGGACACTGGCATTCCTCATCAAGTCCACCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_43602264_43602720_2:0:0_0:0:0_88/1
+AGCAAACTGGAGATGGTAAAAGGCTGTAACTCTCAAAGCCGATCCCCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_29558267_29558774_2:0:0_0:0:0_89/1
+TTTTTGATCTTACAGCACAAGCTATTGCTATTATATTCAAGAATTTATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_59048796_59049203_1:0:0_0:0:0_8a/1
+GTGTACTCTTCAATGTGAGGGTTCCTACTGGAACATGGTCAACCTACAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_31285666_31286194_0:0:0_1:0:0_8b/1
+CAACCAAATTTCACAAACGGAATTATTTAAAATCAAATATATTTAGAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_159055630_159056144_1:0:0_3:0:0_8c/1
+ACAAAACAACTCCAATAGCCATTTTAAAAATCAAACAGTCTAACACGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_163934531_163935036_0:0:0_1:0:0_8d/1
+ACCCTCAGGGAAAGCGTGGCTTTCATCACAGTGTGTGTGAAGCTGTAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_116610918_116611481_1:0:0_0:0:0_8e/1
+TAAAATCATTTTATTTGGGACTGAGTGTTCTAAAGTTTACCACTCTGAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_141208156_141208756_0:0:0_0:0:0_8f/1
+CTCTTTCAGGGATGGTGCCCAGATATCTAGTGTTCGAACCTGCCTCCTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_45492268_45492792_1:0:0_3:0:0_90/1
+GATCTAAAAATCAAGTATAAACATCAAGGTATAAGTTCTATCTAAAGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11755179_11755683_0:0:0_1:0:0_91/1
+ATATATGTTGTTGACTTAAAGGCTTTGAGAAACAGAAATTGTAATGGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_156738022_156738530_2:0:0_2:0:0_92/1
+CTCCAGCCCCTGGACCTTGTGTTATAACACGTGTAAATCATGCCCCCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_95480426_95480839_0:0:0_0:0:0_93/1
+GAAATGTTTCTGGTATACATGAACATATAAATGCAAAACTTGTTTGCCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173460574_173461156_3:0:0_1:0:0_94/1
+ACATTTTTGTAAGCACCCATAAAAATGGATATTGTATAGTCTCAGAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17445381_17445808_2:0:0_4:0:0_95/1
+ACATCGAGACCTTATTTAAGCAAGCCCCCACCCTCCAGAAATCCTTACTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_76540003_76540477_2:0:0_2:0:0_96/1
+GGAGCAACACAATAGAAGACAGAGTTTTCTCTGATACACATTATAGCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_12896019_12896500_1:0:0_1:0:0_97/1
+TTTTCTTGTAATACTTTAAGGGATTTTTGTGTTTCATCTTTGAGGGCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_41708628_41709145_0:0:0_1:0:0_98/1
+GGGGAGACAGGAGAATTCTCACAAGTGCCTGGAAGACCTAGCAGCAAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_106826115_106826660_0:0:0_1:0:0_99/1
+TCCTCCTCCTGCTTCTATGAGGGTGTACTCCCACCCACCTACTTCCACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_13247654_13248181_1:0:0_0:0:0_9a/1
+CACAACTCCTCCCAGGTGGGGTGCAGCTCAAGGACGGGTCAGAGGTGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_117777350_117777861_0:0:0_1:0:0_9b/1
+TCATCTTTTGATACATATGCAGCTAGAGTCAATAGCTCTGAGGTACTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_77191506_77192008_2:0:0_1:0:0_9c/1
+TTAACACTAAGACAATTAAGCCTCATTTACAAACAAGATTAAAGACATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36849743_36850269_1:0:0_1:0:0_9d/1
+GATTGATAAGCCCGATCCAATCTAATCAAAAGAGAGACAAAATCTAAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_148890840_148891366_0:0:0_0:0:0_9e/1
+ATGAAACACTCATCACACTTACTGGATACTTTTGTATACTGTTTGTTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_84671373_84671880_2:0:0_1:0:0_9f/1
+TTCCATATGGATTCTCGGTTGCCTTTCCCTTATCTGTCATCATTTCGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_102434771_102435253_0:0:0_1:0:0_a0/1
+CTGGATGGGACATTTGTATAACTATTGGATGCTCTCCATAAAATCTATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100209819_100210321_0:0:0_1:0:0_a1/1
+GCTACTTATTTAATAATTTGTTATTATCTTTAATTATGTGTGTGTGTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_62044005_62044573_2:0:0_1:0:0_a2/1
+AACATTTTAAATGCGCAACCTAAGAGGCAGCATGGGCCATGGGGCAGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_85132332_85132871_1:0:0_3:0:0_a3/1
+AAAGTCCCACACAATAGTGACATGGCTGCAGTTAGGGAAAATGGAACATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_58843215_58843696_0:0:0_0:0:0_a4/1
+AGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAAAAAAAAAAAAGATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_137975188_137975732_1:0:0_1:1:0_a5/1
+TCTTTTATATAATACACCCTGACCACAGATTTCCTTCCCTCTCTACCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_141967561_141968074_0:0:0_0:0:0_a6/1
+ACCACAATATGAAGAACTGTTTTAAAAAGTTGCAGAATTAGGAAGGTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_8624607_8625140_1:0:0_1:0:0_a7/1
+AAGAAAACCATAGTTTAGTTCTGTGGATGTGGCTGAGAGGTTCACCATGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_138783244_138783650_1:0:0_1:0:0_a8/1
+GGCAAATAACTACATGAGATGCAATTTCCCAAGTTCCCTCTCTCTTCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_52699200_52699639_1:0:0_1:0:0_a9/1
+AAGATATGGGCACAGGGGAAAAATTACTGAATAGAACAGCAAAGGCTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32849205_32849709_0:0:0_0:0:0_aa/1
+AGTGGATGATCACAGTCAACTATTGGATGGATCACACGGCCCCCATGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_182043596_182044137_0:0:0_0:0:0_ab/1
+CAACCATCTGTACAGCTACAGTGTGCTCATACACATAAAATACATAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_136004325_136004842_4:0:0_0:0:0_ac/1
+TAGTCTACATAGAGAGCTCCAGGACAGGCCGAGCTACAAATTGAGAGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_174545541_174546018_2:0:0_1:0:0_ad/1
+CGCCCCATTGTGCATTCGATCTCCCCAAGTGTTTTCATTATTACATGATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_11117502_11117925_0:0:0_1:0:0_ae/1
+CCATCCACTAAAAGTTACAGAACTTAGCTGGCACAATGGACAGAATGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_44177515_44177974_0:0:0_3:0:0_af/1
+ATAATGATCTCTTCATCAGAGGAGCATTAAAAGAAAAAAGAAAGTGTGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_72645507_72646002_0:0:0_0:0:0_b0/1
+GCGCCTAGATTGGGCAGATCTACCACTACACTACCATCTTCCACATCTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_147283777_147284272_0:0:0_1:0:0_b1/1
+TCATACAAGAAGCATACAGAACTCCAAATAGACTGGACCAGAAAAGAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133675964_133676447_1:0:0_0:0:0_b2/1
+ATCACACAGGCTCTTCCCTAAATATTTCTTCATTATTGCGGTGGTTTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114568587_114569130_0:0:0_0:0:0_b3/1
+TTTCAATATTTTTTAGATGACCTATGAATGAATAACTAGGAATTTTGTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_111695385_111695895_0:0:0_0:0:0_b4/1
+TAGCCCCTTAGCTGACCTCTGGCTTTTCACCCTTGCTGTTACTGCAAGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_172273320_172273788_1:0:0_0:0:0_b5/1
+GTCCTCTCTGTCCATAAGGCTCAGGAGTCACAGAAGGTCCAGCTATCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29014340_29014871_0:0:0_2:0:0_b6/1
+GCCACTCATTTACATCAAATAAATCCCCTGTATTCCAAGGCACCGTATTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626521_177627066_1:1:0_0:0:0_b7/1
+CCGTGTGTGTTTCTCTGTGTCTCTCTTTCTTTGTATGTATGCTTCTCTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_110742845_110743354_1:0:0_0:0:0_b8/1
+AATGGGTACAGAAAATGTGATACATTTGCACACTGGAATCCTACTCAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_14101155_14101687_3:0:0_0:0:0_b9/1
+ATACAAACAGAGGTCAATGTCAAACTTCAGCCTCCTTTCTTTCCAGATGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38147934_38148475_0:0:0_0:0:0_ba/1
+TCTCCCCCACCTCTCACATATACATACATGAGTGTAATTCTTAAACATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_84834550_84834957_2:0:0_1:0:0_bb/1
+TATTTGCACAGGTAGTTAATTTTTGAAACAGGGTGTCATGTAACCCGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_94046734_94047311_0:2:0_1:0:0_bc/1
+AAAGTCAGGCTGGTCTGTTGATTTTTACAAATGAAAGGAGTGTCTGTGCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138724568_138725155_1:0:0_2:0:0_bd/1
+TAACATATATATTAATGTTCTTATCCAGAGAACACAAAATAGTGAATTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_105672406_105672966_0:0:0_1:0:0_be/1
+TGGTGGCACACGCCTTTAATCCGAGCACTCCGGAGGCAGAGGCAGGCGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_157814995_157815529_0:0:0_3:0:0_bf/1
+TTCCCATTCTCCAGCTCCACCCTAAAATACCACGTCGCTGACTACAGCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_130059190_130059641_1:0:0_0:0:0_c0/1
+CAGTGCTTCCTCCAATTCTAACATAAGAGTCTCTGACCTGTGACCAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_18604367_18604942_1:0:0_0:0:0_c1/1
+GAACTGAAGCATGGACCTTTGCTGGATTACTCTCTATGTCTTGCTTGGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_160029930_160030407_0:0:0_1:0:0_c2/1
+GCTTGTTTCCTTATCGAAGCCAAGACTACCAGCCCAGGCATGGAACCACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_32417120_32417575_0:0:0_3:0:0_c3/1
+AAATAGCCATGTTACTTTTTAAAGAAGAAACTTGACAGGCTCTAGATTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_91572336_91572825_0:0:0_3:0:0_c4/1
+TTGAGTCATCACATACTGCTGACAAGGAGGCCGTCAAGCCGGTCCACACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_167308006_167308522_0:0:0_0:0:0_c5/1
+CGTGTCCGTCCCCCCCCAACCCCCCGGCTGTTTTTTTTTTTCTTTCTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_53658226_53658697_1:0:0_1:0:0_c6/1
+AATCAAAACAACCCTGAGATTCCATCTCACACCAGTCCGAATGGCTAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75542501_75543075_2:0:0_0:0:0_c7/1
+AGTAATCTACAGCAGAAACAGAAAGGGTGGAGATGACCCAGCATCTGGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_49392954_49393517_0:0:0_2:0:0_c8/1
+AGTGCTCTCTAAAGTTTTTGCCTCTCAGTAGAATCCATTCCCAACATGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_18890524_18891056_1:0:0_0:0:0_c9/1
+AACAATCCTGAAGTGCCTGTGCCATCACGAGCAGGGACATAGTAATCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_13661516_13661931_1:0:0_1:0:0_ca/1
+GTGCGCCACCACCACCCGGCAGTTCTTAACTCTTAACAGGCCCAATTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_69507936_69508419_2:0:0_1:0:0_cb/1
+AATCTTATAGTGTATGGAATATACATCAAATGACAAATCAGATTCCCTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_171186227_171186672_2:0:0_1:0:0_cc/1
+TTCCCGTTCTGGAAAAGAAGAGACCCCTGCCCCCTGCCCCTTCCTGCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_151167139_151167658_0:0:0_3:0:0_cd/1
+AGAGACAAGTCTTGGCTAAGGGAAGCAAAGTGAGAGATTGGGTTCAGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_166490443_166490901_1:0:0_2:0:0_ce/1
+CTTCCTGTCCACATCAATAAGCCGCCATTCTGTGGGCTGCCGACTGACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78053476_78053981_1:0:0_0:0:0_cf/1
+ATAAAACTTGAACTTCATAAAATTCAGATGTCTAGAAGACAGAGACAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_27573317_27573793_0:0:0_2:0:0_d0/1
+TTATGATTGTAGCTTTATCCCAAGAGGCAATCTTAAGATGATGAAATGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_74520986_74521432_1:0:0_4:0:0_d1/1
+GAAGAGTGGCCTTAACGTTACTCTGTTGCTGATAGTGACTTTGAAGTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_194568812_194569255_1:0:0_0:0:0_d2/1
+TTGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_173094678_173095086_1:0:0_0:0:0_d3/1
+TTTGTGTTGAAGTGAAATGTAGATATAATTCAGGTTAAACCTAGGTGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_125473775_125474200_1:0:0_0:0:0_d4/1
+TAAGAAAAAAACAACAAGAATAAAAAAGGGTGGGAGAGATCATGCCATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_60312834_60313394_2:0:0_1:0:0_d5/1
+TTTCTCTTTCATTCTCCTTTTACTACAAGTTATCCACAGAATCTCTTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_21769340_21769783_1:0:0_1:0:0_d6/1
+ATATCATGTCAGTTCTTTTGTGATTGGGTTACCTCACACAGGATGATGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_29011734_29012196_0:0:0_0:0:0_d7/1
+ACAAGTCTTTAGTATTTATTTTTCTAAGCTTGTTTTAATACGTTAGGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_55988735_55989188_1:0:0_0:0:0_d8/1
+CAGAGGTTAGCCGTAGGTCTCGTTCCTGAGGAACTGTCCACCTTGGTCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_143689772_143690244_0:0:0_2:0:0_d9/1
+CATACTGTTTTTGGGCCTGTGCAAGAAAGAATCTGGCATAAAGGCATATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102292799_102293241_0:0:0_2:0:0_da/1
+AAGGTGCTTGCTCATTTTCATAATATAATGCAAAGTCTTCAAGTCTCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_175815890_175816392_0:0:0_1:0:0_db/1
+TTTGGAAGGGTGAATTTAAGGTTACCTTGCTTCAGTCTCCAGATGTGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_65030887_65031423_1:0:0_0:0:0_dc/1
+GTAAAACCAGCAAGGCCAACCCCAACTAAGCAAATTCATATTGGCTCCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_77446136_77446727_1:0:0_0:0:0_dd/1
+AGTCCTTTTTCCCGCTTGTCATTATGGGAGACGAAGAGGAGGCAAATTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_79825884_79826306_1:0:0_0:0:0_de/1
+AATTCATGGCTTCTCTCTTGAAAAACAAATATTATTCTGAAGCAAACTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_142137580_142138145_0:0:0_1:0:0_df/1
+GAACACACAGATTTTTTTTTTTTTACTTGAATCTTGAGAAATAGTGGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77524851_77525306_1:0:0_2:0:0_e0/1
+CAGAAGGTGTACGTGTGTGTGTGTGTGTGTTTGTGTTGGGGGTGGGGGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_26694201_26694676_0:0:0_0:0:0_e1/1
+TCCTACCCAATTTCAAAGCTATATCAGCTTTTTAGATATTTTGAGAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93157579_93158060_0:0:0_1:0:0_e2/1
+TCCTGCAGGCCCCTTACTTGGCTGAGGCACAGTCCCACCTTTTAGAGCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93554302_93554745_0:0:0_1:0:0_e3/1
+TGAAGCAATTCTGATTTGAAATTAGTGCTGCTGGTGATAAAAATGCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_115859373_115859816_1:0:0_1:0:0_e4/1
+TAGTTTTCAGTCAACTGTGAACATACTAAAGGTCAGAAGCCTTGATAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_59908209_59908731_3:0:0_0:0:0_e5/1
+GAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_154628329_154628794_2:0:0_1:0:0_e6/1
+ACGAGGATTAAAGGTTTAATACATAAGCCAAAGACACATTTGCTAAGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38934187_38934653_1:0:0_1:0:1_e7/1
+TGTTTACCCGAAAAGTATTTGATGCTGCCAGAGGTTTAATTAATGACAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_176440703_176441215_3:0:0_1:0:0_e8/1
+GCCTTCTCCCTACCACTTTGGAACCTTCTCAGAGAGGGCAGCCCTGATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_146248574_146249007_1:0:0_0:0:0_e9/1
+TAATTTCAATTAAATTGACATTTATAAATATATTAGGTAATCCAAAGTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_137417062_137417534_1:0:0_0:0:0_ea/1
+CATAGCACCTACCCTTCTGTAAATGAAAGTTTGAAAATAACAGTGTAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_55607180_55607772_1:0:0_0:0:0_eb/1
+AAAGGATAAGATTTAACTTCACTTAAACTTTCATCCTCTAACATCACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_174928179_174928755_0:0:0_1:0:0_ec/1
+TTTACTTTGAAGAGGTCATGGTGGGTGTATTAATCAGAATTCTCCTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_113923154_113923648_3:0:0_1:0:0_ed/1
+AGAGCTGGCAGTAGACCTTAGTTGCCCTTGGTCTTAGCTGCATTGCCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_78423064_78423594_1:0:0_0:0:0_ee/1
+ACTCACAGTCTGTCATGGACACTCGGCCTGTTTGTTACTGTTATTAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_154582561_154583019_0:0:0_1:0:0_ef/1
+TCAAGATAAATCAGGGATGAACATTAAATACTGCCGAAATTACAGGGCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_181723357_181723842_1:0:0_2:0:0_f0/1
+AAACTGAATTCTAGAGATTTCTCAAGAAATAAATCAGAGATTCTGTCCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176206787_176207249_1:0:0_1:0:0_f1/1
+TTTCCGTGGGTCGAAGCATGCCCCTCTCAGAATCTTGATGACACCGCATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_156026308_156026788_0:1:0_2:0:0_f2/1
+AAATTTGGACCAGACAGTATATAAACAATTTTCACAGTGTTTGTATTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_55128175_55128671_1:0:0_0:0:0_f3/1
+GCCAACCAACTTCAGCTCCTTCCTCTTTCAGGAAAGATCACAACTTACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_184447109_184447646_1:0:0_1:1:0_f4/1
+CAAGCCCTTCCTGCTATCCTTCAGGAAGAATGACACGGTTACAGCTCCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_194617734_194618226_0:0:0_0:0:0_f5/1
+GAACAGGATGGGTATATGTGGAGGAGTCACTTTCATTTAATGTACCCCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_80810218_80810755_0:0:0_0:0:0_f6/1
+TTCCCCACCCATCCCGGCTTTCCCACCCTAGCATTCTCCTACACTGGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_144296368_144296930_2:0:0_2:0:0_f7/1
+TGCATAGGAGAAACTGGGAAGGCGGGTAGCACTTGAAATGTAAATAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_108312503_108312946_1:0:0_2:0:0_f8/1
+TAAGATCAAGAATCAACAAATGGGACCTGATAAAATTGCAAAGCTTCTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78228179_78228640_0:1:0_0:0:0_f9/1
+GGGAAAACAGTGAAAGTCACTTTGTGCTTTGGGGAGGCCAGGAGAAGCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_52088998_52089426_1:0:0_1:0:0_fa/1
+TGATTTTCTTTGAACTGATTAGAGGCATTGTAAGTTTTTTTTAGGATAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_30782403_30782942_1:0:0_0:0:0_fb/1
+GTGAGTGTGTGCCTGCTTTACATTGCCTCCAACTCCACATCACTTCCTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_6435675_6436268_3:0:0_2:0:0_fc/1
+CTGTTCTCTCCGAGGCGCAGCTTGCTCAGACTCTCCAAAAATACGCTCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_164237997_164238538_0:0:0_0:0:0_fd/1
+CAGGAGCCTTAACCTTCTCTTCTCTCTGAGAGGACTTTATATAAAACAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_187097969_187098475_2:0:0_2:0:0_fe/1
+AGAAAACAGGGGGTTGGGAGCAACCCTGTCCACTGTGTCGAGCATTGGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44694856_44695375_3:0:0_1:1:0_ff/1
+GTCGATAACTGTCAGGTCCATTTGTTTCATAACTTCTGTTAGTTTCACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_111782668_111783223_1:0:0_3:0:0_100/1
+ATTGCTCTGTAGTTTATAACTGTGAAGAGGGCTATGTGGATAACTAATTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_94206847_94207360_1:0:0_1:0:0_101/1
+TATAACAGAGATACCACGAAGCCCTAATGTTAAAACTTACTTTTAGGAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132119789_132120286_3:0:0_1:0:0_102/1
+GCATAGACCTCTGTCTTCAAGAGCAGGGCATAGGGCAACTAACACCATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34226734_34227203_0:0:0_0:0:0_103/1
+GAATTCAAAGCTAGCCTGGTCTAGAGAGTGAGTTTCGGGACAGCCAAAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_138105716_138106319_4:0:0_1:0:0_104/1
+CTACTATCTCAAGAGAGCTGTTCATGTGATAGAAATCAGCTAGTGCAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_126030856_126031342_1:0:0_2:0:0_105/1
+ATACTCAGAACCCAGTTTTTAAATGTCAGGCATGGTGGCATTTGCTTAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_118807485_118808058_0:0:0_1:0:0_106/1
+AGCCACATTTATCCGTGTGTCTGTTCTCAGACAAGCCAGTGGGGGCCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_19849114_19849606_2:0:0_0:0:0_107/1
+AACTTTCCATTGTAACAAAATACTGGACCAAAGACACTTGAGGAAGGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_66877733_66878136_2:0:0_1:0:0_108/1
+TGAAGAGATGGCTCAGGGTTAAGAGCCCTGAGTGCTCCTCCAAAGGTCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_132522495_132522987_0:0:0_1:0:0_109/1
+ACTTCCCAGTTGACTTTGATAAGCCTGGAGGTCACTACCGGAGAGCCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117050436_117050942_0:0:0_1:0:0_10a/1
+ACGGGTGGGGGGGCGGGCACTGGTTAGTGCCCTATAAGAGGAACTAACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_125967212_125967705_0:0:0_0:0:0_10b/1
+CTGTGCTCAGCATCCTCCTAACTCCTTCTGACAGAGGCACCGGGTCACTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69313718_69314189_1:0:0_2:0:0_10c/1
+CACTGTTTCCTGTATCTAATCCATATTAGTGAGGACTATGATATTCAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_60897368_60897871_1:0:0_1:0:0_10d/1
+CTCAGCTATTAAAAACAATGAATTTATGAAATTCTTGGAACAATGGATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_174325015_174325549_0:1:0_2:0:0_10e/1
+CACATCATTACTTTAAATTTATGCAAATATCATTTTTAAAACTTAATCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_85055965_85056468_2:0:0_0:0:0_10f/1
+CCATCTATGGTCATTGAGAGTTTGGCTGGTTATAGTAGCCTGGGCTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_131415777_131416249_5:0:0_1:0:0_110/1
+AAGTTCGCGAGGGCTGACCAGAGGGCCACAGCGGGACAGGAAGGACCCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_67136277_67136702_3:0:0_0:0:0_111/1
+CTTTCACCATCATAAGATATTTTTGGAGCCTCCATCCTGTCAAACAGATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_8402131_8402528_1:0:0_2:0:0_112/1
+AATTGTCCCCTGCATCCTATCCGATCACCATGGACTAAGGCTGATCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_155126875_155127345_1:0:0_3:0:0_113/1
+CGACAGCAAGTGAACGCATTGGCGTTTGGCATTCCTCTCTATGCATCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_93916438_93916928_0:0:0_0:0:0_114/1
+GCAACCTTGTCCAGAGGGTGCTCAGAGCTGGCTCCTGGCTAACAGTGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_135734641_135735118_0:0:0_0:0:0_115/1
+CCCCTGCACTGGCAGGTCCTTGGGTTTCACCCATTCCCCGCTTCCCCCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_44391025_44391499_0:0:0_1:0:0_116/1
+GGGAACCCTGAACCCCTCAGGGTGGCGGGAGGCGTACATGGAGCCAGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_110722550_110723095_2:0:0_4:0:0_117/1
+AATCTATAAACCCAATAATAGAAAAATGAAAAAATTCTTCAACACATGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_185586471_185586808_1:0:0_0:0:0_118/1
+TGGCCATCAAAATTCCAGAAGGCTGCTTTGTAAAAACCGTTCATTCTCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_182936908_182937483_1:0:0_2:0:0_119/1
+ATTGAGCTGTACTTAAGCACAATTAAAATGTAAAGATGTTGATTCCTGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_136882207_136882635_0:0:0_2:0:0_11a/1
+CAGGAGCAAAGCTCTCCCTAGCTGGACTGGTAATCTGTTGTCAACTTGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_22027558_22028086_0:0:0_2:0:0_11b/1
+TAATGTTTGCACATAAGTCTCTGCATGTTTTCCCATTGGTTCTTGTTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_101069088_101069523_0:0:0_0:0:0_11c/1
+GCTCTGGGGATACCGGTTAGTTCATATTGTTGTTCCTCCTATAGGGTTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_133430180_133430643_0:0:0_3:0:0_11d/1
+TTGGAGCTTGAGTAGTCGATAGTTGTGAACCACCATGTGGATGCTGTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_141505317_141505766_0:0:0_2:0:0_11e/1
+AATGGAATCTTCTGTACCTGAGATTCTCTCTTTCAACTCTTGTATTCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103387516_103388014_1:0:0_1:0:0_11f/1
+TGAAGTCTCTAAAGACCAAATCATTCCCTACCCGTCTCTCTCTTTTGTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_134753416_134753860_0:0:0_1:0:0_120/1
+GTGCAGCCAGGGCACCTAGCCCATGGCCTCCAGCCGGACTGAGACAGCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_168048225_168048764_3:0:0_0:0:0_121/1
+AGTCGGCATCCTCCCCTTCTTTCTAAAGACTCCCTGTACCAACATTTCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_15110325_15110842_0:0:0_1:0:0_122/1
+GGAACCTATAGTTTCCAATGGTCATCAAACTGTAATTAAGTAATTTATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_71511848_71512298_1:0:0_1:0:0_123/1
+AAACACTGGGAGTGCCTGCATAAATCTTTTACCATAAATGGTAGGGAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_37275066_37275622_2:0:0_0:0:0_124/1
+ACCCCGAGTTCCCCAACATTAAAAACATGATCATGCCCGGAAGAAACAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_191970326_191970894_1:0:0_0:0:0_125/1
+TATAGAACCTGGTCTATGTACCCTGAATCTGGATACGGCCTTCTGCCTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_137258018_137258449_1:0:0_1:0:0_126/1
+AACCTATGTTAGGCTGGAACCCCTGCTTGCCCTACACAAGCTGGGAAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_163885263_163885763_1:0:0_0:0:0_127/1
+CTTCATGTATTTAAAAGTTACTTATTTTTCTACCAGTGATCACTGTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_95122061_95122611_1:0:0_2:0:0_128/1
+TTTGGGTCAAGTTCTCAGGCTTCATTTTTTTTAGGTGGCGACCAGTCCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_191245641_191246131_1:0:0_1:0:0_129/1
+GTTCAATCCTACCTCTGTTAACAGGCAGCCAGATAATTAATCTGTCATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_11721955_11722368_1:0:0_3:0:0_12a/1
+ACATTTGTTAAATCAACTGAGAGATGTAGACACTCTATTAAGTCACCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102954712_102955237_1:0:0_1:0:0_12b/1
+TTTTTCTTTGATTGGTGGTTTAGTTTCTGGTAGCTCTGGGGATACTGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26914346_26914925_0:0:0_1:0:0_12c/1
+TTTAGATGATCCCAAAATGAGATTTAGAATGTCTTCCTTTTGCACTTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_151053369_151053909_1:0:0_0:0:0_12d/1
+GACTTTAAAAAAGCCTCTGAGGAAGCAACATTGAAATTGAAAGTTGCAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93621447_93621970_1:1:0_1:0:0_12e/1
+GCCCCTGGAATGGGCCTCATAAAAACTCTAGGAGGGCTTCTGCTGCCCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_13530953_13531445_0:0:0_0:0:0_12f/1
+AGAAAAAGGTCCATTTCAAAGAAATATTTGTTAGTAATTTAGGACAGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_154530120_154530631_2:0:0_4:0:0_130/1
+ATGCTTTCTAGTCTCTAAATGGCCTCCTGAAACCAGAGAGTGAACTTCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_100109085_100109588_0:0:0_2:0:0_131/1
+TTGTCATTATTTGTCTGGATGCATGTTGGCATGAAAGTTAATGATGTGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_150348101_150348543_0:0:0_0:0:0_132/1
+AAGGAACTGAAATCCTGCCCTGTAGAAAAAATTGAGCCTTTAATGGCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_8725925_8726392_0:0:0_3:1:0_133/1
+ATTCAGGTGACAACATATTCAGTTGAGGATATGGAGAAAGATGACCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_189147844_189148204_2:0:0_1:0:0_134/1
+ATTGAGAAATATGCAGGAAAGATGGAGTAACAAAGATCCTTAAAAAAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_45618673_45619149_2:0:0_2:0:0_135/1
+ACACTGCATGATATGGAGTCTATCCCAGGCATCAGTGAAGAGGCCAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_104062147_104062721_1:0:0_0:0:0_136/1
+ACATACATATATATACATATATATATATATATATATATATATATAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138405158_138405766_1:1:0_1:0:0_137/1
+TCAACACAATGACCCTTCTTGCTTTAGAGTCCTGCAGTTCATGTATTTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_115548969_115549503_0:0:0_1:0:0_138/1
+AATTGATGCATCCCCTCTTGGTCCCCTCTCACACAGTCACTACCCCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_195151172_195151687_0:0:0_0:0:1_139/1
+ATTTGGGGCTACTGTTGACTCTGGAATGTGAGGATGGGTATACCTTGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138103424_138103925_0:0:0_0:0:0_13a/1
+CTACTAGAGAAACTACTTCCTCACGTATTATTGAGACTTCCATTGTGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_84481564_84482032_1:0:0_0:0:0_13b/1
+GTTACAGAGACAAAATTTGGAGCTGTGACGAAAGGATGGACCATCTAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_180211651_180212100_2:0:0_1:0:0_13c/1
+AAAGCCATCTGTTTGACATGAAAACGGGGGAGACACATGATTTGGGAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_19484875_19485375_1:0:0_0:0:0_13d/1
+CAACCACTCTGGAAATCAATCTTGTGGTTCCTCGAAAATTGGACATAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_8815773_8816268_0:0:0_1:0:0_13e/1
+AAGTTGTTTCCATTAAAAAGTACTGATTTTGAAAACTAATAAGTTAAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_118367902_118368405_1:0:0_0:0:0_13f/1
+AGTATCTCAGAGAACTCACTGTATAACCCAAGCTAGACTCAGAACCTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_83281820_83282310_2:0:0_3:0:0_140/1
+TTTTACCAGTTCTTCATTTGAGTCAGGGTCTCTCTCAAACCTGGACCTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_24810903_24811377_2:0:0_0:0:0_141/1
+ATAAACAAGGCTGCTATGAACATAGTGGAGCATGTGTTCTTCTTACCGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_24847990_24848482_1:0:0_1:0:0_142/1
+GTGCTTACAAAGGCAGGAAGATTCCTGAGTTCAAGGTCAGCGTGGGACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_25453923_25454484_1:0:0_2:0:0_143/1
+CATCTGTGCTTTATAGTGCTTCTCATTCGCTGACAGGGATAGCCTCCAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_35396075_35396608_0:0:0_1:0:0_144/1
+TTAGTGGAACATCCCTGGCTCCACTCTGTGTGTGTGTGTGTGTGTGTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_184356181_184356676_1:0:0_1:0:0_145/1
+GGGAGAGTAAGTAACTGCCTTCTTGTATCAGCCCCAGTTTGATGCTTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_87890172_87890679_0:0:0_1:0:0_146/1
+GGAGCAGAGCTGATGGAGCATGGATCACTGTATGATCAGAGAATTAATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192825121_192825655_0:0:0_3:2:0_147/1
+CCACATGGTGGCTCACAACCATGAGTTTCAAGGAATCTTCTGGCCTTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_29477154_29477657_0:0:0_0:0:0_148/1
+CTTCTCAGCCATTTGATATTCTTCAGGTGAGAATTCTTTCTTTAGCTCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_68360607_68361138_2:1:0_2:0:0_149/1
+ATTGTTAGGCAGAGATCCAATATATGAAATTGTGCTTTTCCTGTTGATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_90679374_90679891_2:0:0_4:0:0_14a/1
+GCCAAGGCACTTGTGTGTTGGTTAGAAGATAACTTTTGGAAGACAGTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_90921852_90922384_0:0:0_1:0:0_14b/1
+CTGGATGAGGCGCCGAGATGGGGAAAAGGTTGGACCTTTCCACGCTCACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_144744406_144744790_0:0:0_3:0:0_14c/1
+TATATCTTGGGTCTCCTATGTTTGGGGCTAATATCCACTTCTCAGTGAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_157579434_157579959_0:0:0_1:0:0_14d/1
+CATAATGTTGTTCCATCTATAGGGTTGCAGGTCCCTTTAGCTCCTTGGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22354013_22354577_0:0:0_2:0:0_14e/1
+TTCTGTAGCTGATAATACATCATTGTGTTGGCATATCTCATTTTAATACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_14011029_14011557_0:0:0_1:0:0_14f/1
+AAAAATGTCACATGCAGAAAACAAAGACGCCTTCCTTGGCAAACACTGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130418472_130418955_2:0:0_2:0:0_150/1
+TGACATGGATGTCCGAAATTCCGATGGTGAAACACATCACTATTATTATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_150912771_150913298_1:0:0_0:0:0_151/1
+CTGTTTAGAAAAGTTTTATGATGTTTAGAAATCATGCATGCATAATACTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_122600000_122600452_0:0:0_0:0:0_152/1
+CCCCATTTCAGGGAACAGTAAAGGCAGGAGGATCCCTGGGGCTTGCTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_172852130_172852552_1:0:0_2:0:0_153/1
+AAAAATGTACAACATCCTTAATCATCAGGGAAATGCAAATCAAAACAACG
++
+22222222222222222222222222222222222222222222222222
+@chr1_58219252_58219809_1:0:0_1:0:0_154/1
+CAGAGGAAGCAGAAGAGATACACTTCCATGTCGGGTTCCTAAGTGATCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_154116562_154116985_0:0:0_0:0:0_155/1
+TGACCATGCCAACCCAGCTCGAGAGCTTTTTTCCTCTCTTTAACATCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_169424620_169425179_1:0:0_0:0:0_156/1
+ATAGTATGGTGGATGAGTTAAGAGTAAGTTTCAAAGCTGGGACAAATGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_72776580_72777093_1:0:0_0:0:0_157/1
+GATATCCCTGAGTTGTTACTCTGTTTCATCTGGGCTGTTCTTAACTCCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_102420738_102421205_2:0:0_1:0:0_158/1
+CATTGCCAACTCTGACACATGTCAAGGAATTCAGAGTAGAGAGCATATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_148315363_148315906_2:0:0_0:0:0_159/1
+CATGGAAGGAGTTCCAGAGACAAATTTTGGAGCTGTGACGAAAGGATGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93257911_93258453_0:0:0_1:0:0_15a/1
+ACACCGGGCAGTTCTCATTGCATTGCAGCGAAGGACTTCTGCCATGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_94169994_94170446_0:0:0_1:0:0_15b/1
+CCTTGACCTCCTTTTCCTCAGGTTCTTCTCGTTTTAAATGAAAAATTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_126263407_126263894_2:0:0_2:0:0_15c/1
+GATTAGACTCTCGCTGCATTATGAAAAAAAAATTATGTGCATGAAGGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_42763327_42763896_1:0:0_0:0:0_15d/1
+GTCTAAACATTCTAGTCATCAGAATAAAGTCAGAAACAGAGGCTGGGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_127932894_127933379_0:0:0_2:0:0_15e/1
+GTCAGCAGTGCAGGATTATCTATCTATCATCTATCTATCTATCTATCATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_83608654_83609158_1:0:0_3:0:0_15f/1
+AGACACAGTAAGGAGCAGAGACTGAAAGAAAGGCCATCCATAGACTCCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_47669914_47670464_0:0:0_0:0:0_160/1
+CCCAGGAGTTGTATAGCTGGTGCTTGAGGCACACTTGCTGAGAAGAGGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133731323_133731869_1:0:0_2:0:0_161/1
+GATGCTTGTGAGACACTGGGCAATGCCACAGCCATTTGCTCGGATAAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_133255321_133255920_0:0:0_1:0:0_162/1
+TCTGGAAAGGTTCAGGCTCAAGGAACTGGAGACAGATTTAACCCCACATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_23328420_23328852_0:0:0_1:0:0_163/1
+AGGAAGAGAAAAGATATGCTAAGAAACCAGATGACAGGCTCCAAGAACGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53072730_53073291_2:0:0_0:0:0_164/1
+TACGACGTCCACTTATGAGTGAATATTTTCAGTATTAATGTAAGGTGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173130259_173130757_3:0:0_2:0:0_165/1
+AATTATTTGGAGAGCACTCAGCAACTAAGAAAGTGATTTCGTACACAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_87397192_87397710_2:0:0_1:0:0_166/1
+GATGGGGTTTCCTTTCACTATTTAATAGAGAAATATAACGTTACTTTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_187438711_187439219_1:0:0_1:0:0_167/1
+CATTTGGTCTGGACAGGACGGCAATAAATAAATAAATAAATAAATAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_123461089_123461580_0:0:0_1:0:0_168/1
+ATACAGCTTTCTGCATGTGAGTATTGTATGTGCACATTGACGCCTAGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_181088135_181088642_2:0:0_2:0:0_169/1
+ACACTTTTTTTAAAAAATAAACATATTTTTATAAAACAAATGGACTATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_167764494_167764902_0:0:0_1:0:0_16a/1
+CTTTTGCTATTGTTCTATAGTATGCTTCTCCAGTGTGAACTTTGTATATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157283727_157284210_1:0:0_0:0:0_16b/1
+GCACCCCAGGAGCTTGACATACCGTTCCCTAATTCCTACCTCTTCCCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_156428357_156428913_4:0:0_3:0:0_16c/1
+TCTCCCTTCCAATGTAGGACTGATCATGGCCACCCTTCCCCCTCACCCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_27945156_27945679_0:0:0_2:0:0_16d/1
+GCCTTGTCTATCTACTGGAGGTCATCTCTTCAATTTCCATCTCCCCCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_190959090_190959565_0:0:0_0:0:0_16e/1
+TATTCCCTAAATAATATGGAGTTGAACAACTATCAAGCTTCAGGCATTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_163184140_163184589_0:0:0_1:0:0_16f/1
+ATTAGACACCCCAGTCAGAAAAATGATGCACGTTAACGAAGATAAATGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_104189461_104189906_1:0:0_1:0:0_170/1
+ATTGAAAAACAGAACCTCATAAGATGGAAAGCTTCTATAAGGTAAAAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_77562742_77563170_2:0:0_0:0:0_171/1
+TATGGTCCAAAATAAAGCTCTCTTTCCTTATGTTTCTTGGTCCGAGTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192763088_192763581_0:0:0_0:0:0_172/1
+TGTCAGAGTATTCTATCACATCAATAGGAAACGAAACCAACGCCCACTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_36839841_36840369_1:0:0_1:0:0_173/1
+CAGAGGGTAAGTTTAATGTTCATTTTGGTGGGAATTAGTGCCTAGCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114603035_114603542_0:0:0_0:0:0_174/1
+CACTGGTGAGCCTTCCAATTCCGGATTGTAATTCATTCCAAATATTGTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_57790506_57791066_2:0:0_0:0:0_175/1
+GTGGAAACTTGAAGTATATTGGGGTATACCCGCGCCAAAGGACTATTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_35650713_35651282_0:0:0_0:0:0_176/1
+TAAGAGCCAGCTCCCACCTCCAACTCACAAAAAAAAAAAAAATCAACAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_9711969_9712380_0:0:0_3:0:0_177/1
+TTATTTTCTAGCTTTAAAAAACAAAGATTTATTAATATATTTATTTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_89016556_89017046_1:0:0_0:0:0_178/1
+AATAGTTAATATACATATTATGTTCTCAGAAAATGCTAAGAGTTTATATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132197564_132198148_2:0:0_2:0:0_179/1
+CCAACATGAGTTCGGAGCAGCAATCACATAGGAATTAAAAGCCATAGGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_104335733_104336245_1:0:0_3:0:0_17a/1
+AAATCCTTAATAGTAATATTACTGTATTAATTTTTTTACCTTATATACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_75633066_75633602_2:0:0_1:0:0_17b/1
+ATTCTTATGTTTATTGGTTGACATTGGCTGTCAACTTGACAGGATCTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_189869166_189869657_0:0:0_1:0:0_17c/1
+TCGGCTCTGTGCCACGGTTGGAGACCCCTGTTTGTGGTGTGGTATCGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_27940779_27941192_2:0:0_0:0:0_17d/1
+CAATAAAATACTCACAAACAGAACCCACAAACACTTCAAAACAATCATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_116796056_116796571_1:0:0_1:0:0_17e/1
+GGCTATTCTGAGGCCTCTGGTAACTATATAGCAGAAGACTTCCTGGTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_20487571_20488054_3:0:0_1:0:0_17f/1
+AATGGCGTGGAACTTGAGCCTGCGGTACATAGGTAAGCAGGCTACCCGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_70106451_70106893_0:0:0_2:0:0_180/1
+TATGTCAATAGTTATAAACAATGTCAGTGTAAAGCAAGTCTTGTGCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_138350547_138351128_3:0:0_0:0:0_181/1
+ACCTTTTTTTTTCCCTCTGTGTATTTTTTTTTATTCCTCCTGTATCTCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103571822_103572343_2:0:0_1:0:0_182/1
+GCCACCCAAGTGCTCGACTTATACTATACGTAGGACAACCTTATACATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_185391115_185391738_5:0:0_0:0:0_183/1
+TTGAAGATCTTTGAAATGTGAGTAAAAATGAGAAATTTAACAGAAAGTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_121389447_121389902_0:0:0_0:0:0_184/1
+GCCCATTTCCTGTTGGCTGCACTTGACTTGGGGTGTTTAGGATCCATTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44088278_44088819_1:0:0_1:0:0_185/1
+AATACTTAAAAGAGTGAAGAAATTGTTTTTCAATGAATCAACTTTAAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_57600248_57600747_0:0:0_3:0:0_186/1
+GTTCGGAACTCATAAGCACATTGAGACAAGGCCATAGCCAGTTCAGACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_105765709_105766274_0:0:0_4:0:0_187/1
+ATGGTGACGTAATACTGACAGCTGCTTAGAGCTGTGGCCCTGACCTGTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_158039847_158040318_0:0:0_1:0:0_188/1
+CCCCTTGTCTGAATACATCTGCCATCCCAACCAGCCTCAAGGAAGCACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_100649250_100649781_0:0:0_0:0:0_189/1
+TTAAACACTGTCTATTCATGTATTCATTTGTGTACTTCAATGTAAATGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_92627120_92627576_1:0:0_1:0:0_18a/1
+ACAGTGGAAACCAGCCATCACTGATATGCTGGACCAAGATGGAGAAAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_47045474_47045999_2:0:0_2:0:0_18b/1
+GCTAGGTCCAGGTGCTATCCTCTTCACTGACAGGTGTAAGAATCTATTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_58859721_58860237_3:0:0_1:0:0_18c/1
+GTGCAGAGTGTCAGCTGTGTGGGAACCTCACTTCCCTCTTCCCTTAACCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_38899259_38899748_1:0:0_2:0:0_18d/1
+GACAGTTAATGGGGAGTAGACCCCATTATCTCCAAGGCTGTTCTCCTGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_43169971_43170448_3:0:0_0:0:0_18e/1
+CAGGTGAGATAAAGAAGAGAAAGTAGAAGGGCTTATCTGAGCCACAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_169159076_169159522_0:0:0_2:0:0_18f/1
+TTTACATTGCTGACAAATTCATTCGGATACCTGTGTGAAATTTGGATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_14622737_14623201_1:0:0_0:0:0_190/1
+TCTTCATCTTGGAACCTGAATCGTGTTCCATTCCAAACCAAAGGAGGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26821729_26822157_1:0:0_3:0:0_191/1
+AGTTATCAATCATTTTACTTTCTTTTAAGATGTACACCTGAGGTGGTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_146737011_146737509_0:0:0_0:0:0_192/1
+AATATTTTCTAAGATTCAAAATTGTGTATTTTATTATTGTTTTAAAAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_132937628_132938130_1:0:0_0:0:0_193/1
+TCAGGGAGATTTACCAGAGCAAACTTGTCGATGGAGACCAGTTCCTCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_108674541_108675003_0:0:0_0:0:0_194/1
+TGGTTGTCCAGTGTCAAATAGTCATTCCTGAGCATATATATGCTAGACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_155314929_155315340_1:0:0_2:0:0_195/1
+AGGAAAGGAATTTTAATTATAACAGTATCTAAAAGAATTAAACATTTAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_76995369_76995845_0:0:0_0:0:0_196/1
+GGGTTGCAGATCTCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_88758655_88759125_1:0:0_1:0:0_197/1
+GAAACCTCTGTCTGCTGCTTTGTCCAGTTTGACCTCCTTCTAGCATCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_179447008_179447452_1:0:0_1:0:0_198/1
+TGGTTTTAATAAACCTGGCCCGCATAGGCCCATAGGGAGTAGCACTATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_70539778_70540384_1:0:0_0:0:0_199/1
+GAAAAAAGTGGCCATGAATTTGGAAGAGATCAAGGGAGGGGTATATGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_171297998_171298490_3:0:0_2:0:0_19a/1
+GTATTCTAACGCGACTATGCTGGCTACTTCCCGGCCATCTGCCCCTTCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_4703882_4704398_1:0:0_1:0:0_19b/1
+CAATTGAACTCTGCATCTGGTGAGGTATTTTACACCCATTTTTGTAGCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_148373552_148374029_0:0:0_2:0:0_19c/1
+TTCCAGCATTTTCAATATACACTGCACATGTCTTTGCTGTGGTACAGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_165037832_165038374_1:0:0_2:0:0_19d/1
+TAGTGTGGACACCAACTGCTACAGATGTGCCAAGCCTTCATCTCAGGTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_117911191_117911633_0:0:0_2:0:0_19e/1
+GTGAACTCCAGAAAAATCAAATAAGCCTATTAAAAAATGGGGCTCAGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_101942751_101943298_2:0:0_2:0:0_19f/1
+CACCTAATGTTTCCTGTTAGATTACACTACTGATTTATGTTTTCACAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_159291114_159291545_1:0:0_0:0:0_1a0/1
+TATTTGCCTTTATAAGAGCTGCCATGCTCATGGTGTCTCTTCATAGCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26628880_26629394_1:0:0_1:0:0_1a1/1
+AGCCATGTGAATGATTGAATGCGTGAATGAATAAATAAATAAATAAATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_18997387_18997869_1:0:0_1:0:0_1a2/1
+ACTTATTAGTTTTCACTGAAGCTAACCATGCCATTGCTTCCTATTTTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_39575593_39576071_1:0:0_2:0:0_1a3/1
+TCTTCCTGTACTGCATTTTTGTTCTCGTTCAGTTATGGTGTGCATGCGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_5509844_5510306_2:0:0_1:0:0_1a4/1
+GGATCTTCCAGCCCAAAGTTGCAAAGTCCTTCCACAGTCCTCCCCAAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_109704460_109704956_1:0:0_0:0:0_1a5/1
+TAATTACACAGGAACCAGCAAACCTGCCTGTAAAATGGTGAAGGTTTCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_156587931_156588493_1:0:0_1:0:0_1a6/1
+AGTCCTCCTACAATTTGATATGCCAAGGCTGTTTGATATCCATGGGAGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176610586_176611106_1:0:0_0:0:0_1a7/1
+AGTGAGGCTTCTTGGTTCCTCCTTTTTCCTGCTCATTGGAACATATTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_180872448_180872981_1:0:0_3:0:0_1a8/1
+AACAGCAGCTGGGCATGTTGGCCCACGCCTTTAATCCCATCACACAGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_26474215_26474717_2:0:0_1:0:0_1a9/1
+TGGCACGAAGCAGCACAAGCGCAGGCCCGAGCAAACGCAGCTGCTTTGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_104541278_104541749_1:0:0_0:0:0_1aa/1
+AAAAAAATTAAAAAGAGAAAGAAAACAGATGGGGACACTTTCTAGAATGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_67015960_67016373_2:0:0_1:0:0_1ab/1
+TAGTTTTGCCGAGACAGAGTAGGCTCGTCTTTAATATTCGTTTATCTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29940243_29940732_0:0:0_1:0:0_1ac/1
+ACTGCACTGAAGCTGTTTATCAGGTTTAGGAGTTCTCTGGTAGAATTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_193079402_193079850_1:0:0_6:0:0_1ad/1
+AGGACCCAGACTTGATTCCCAGCATCCACAGGCAGTTCCCAACCACCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117439972_117440528_1:0:0_0:0:0_1ae/1
+CAGTACCAGGAGATTTCACCCCTGCTTCTTAATTCTGAATACATCTATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_177239334_177239795_2:0:0_1:0:0_1af/1
+TTTTGAAACACATGGCTAGCAGATACTAGTATAGCAGTAGTAGACTAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_158414545_158415096_3:0:0_0:0:0_1b0/1
+ATTGTAACAAGTACTTTTTTTTTCTGCTGAAATAAAGCCATTACTGGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_97093485_97093964_1:0:0_0:0:0_1b1/1
+GTACACTGGCTGATTTAATCCCACAGTTTTTTTCTTTATAACCTAATGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_67614138_67614777_0:0:0_0:0:0_1b2/1
+GGCCTTATAGAAACACTAAGTCCTAAATATATTTCTCAAGGGAATTTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_153549562_153550076_0:0:0_1:0:0_1b3/1
+ACGCGGGTCTGCAAAGAATCCCCGAGTGTCACTGGCCCCAGGCGGCAGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_55425424_55425904_0:1:0_0:0:0_1b4/1
+CAGTTATAAGTGATGGGCTAAGAGGATGCTATGTGTTCTATGAAAGGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191019412_191019908_2:0:0_1:0:0_1b5/1
+ATATGTGTGAGTTGGGTTCTGTGTCAATGAGTGCAGTGCCTATGGAGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73180421_73180945_2:0:0_2:0:0_1b6/1
+AGCAGCCTACTTCCAGCTCAATATGACTTCATTTTAACTAGTTTATCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_38129466_38129932_2:0:0_2:0:0_1b7/1
+CGCGCCGCCCCAGGCCACCATTCCCGGGCCCAGCCTCTTCCTCGGGCCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_133540103_133540570_0:0:0_0:0:0_1b8/1
+ACAGAGAAACCCTGTCTTGAAAAAACAGAACAAACAAAAAACCAAGCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_184916633_184917139_2:0:0_2:0:0_1b9/1
+GCTAGGACTCTTAACGACCTTGCCAGCCCTCTGTACGAGTTACAGTTAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175669652_175670114_1:0:0_1:0:0_1ba/1
+AGACAGACAGCAATTTAAATAGGCCTCTGTCCAGCAATGGGGAATCTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_8296849_8297319_1:0:0_0:0:0_1bb/1
+ATAACAGTAGCAAGAAATAAAGTATAATGTGAAATAAGTTAACTTCTATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_152905590_152906078_1:0:0_1:0:0_1bc/1
+TTTGTTTGGTTGTTTTAGTTTTCAGTCTGTTTTGTTTGTTTGTTTGTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_114902352_114902833_0:0:0_0:0:0_1bd/1
+CACCCCAGTCCCCTACCCACCCACTCCCACTTTTTGTCCCTGGCATTCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_192964279_192964734_0:0:0_0:0:0_1be/1
+GTAAGTGTGTGTGTATGTGCAGACAGAGACTAGAGAACAATCATGGATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321189_38321768_1:0:0_3:0:0_1bf/1
+GCCTCAGTGTAACAGTTGGCAGCTGTTCCGTGGGAACAGTAACCCATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78900626_78901065_0:0:0_0:0:0_1c0/1
+ACTTTAAAACACAGTGAGTGGGCAATAACACTTAGTAAGACCAGCTATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_113540760_113541176_0:0:0_3:0:0_1c1/1
+TTCCCACCTCAATACACATACACACACACACACACACACACACACACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_130677359_130677835_0:0:0_1:0:0_1c2/1
+GAGCTGAAGGGGTCTGCAACCCTATAGGTGGAACAACAATATGAACTAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_180204210_180204758_2:0:0_0:0:0_1c3/1
+TGTGGCTCAAACTCCTCTCCAAGCTGACTGATTCCATCTGGCTTCTCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_192984278_192984850_2:0:0_5:0:0_1c4/1
+GAAGTGTTGTGGCAGTTTATTTGCTTTGCGTTGTGATCTAAATCAGACCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_176155520_176156071_0:0:0_4:0:0_1c5/1
+GAAAGAGGAAGCTGAAAGCTTGTAAGAGCCAAAGAAACAGAGTTTGCTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_11299746_11300227_3:0:0_1:0:0_1c6/1
+CATTCTTTCCTTCTGAAGGATTTATGATAATATTGCCTGTGCATATTATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_40475921_40476533_1:0:0_0:0:0_1c7/1
+GTCATAGTTGTTTACTAGACACAGAAACGTCTGAGTGTCAGAAATATGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_161162459_161162939_0:0:0_0:1:0_1c8/1
+ACAGAAACTCGTCCCACACAGTAACCCTTAGGTGCATTTAGCTCTCAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56968239_56968712_1:0:0_4:0:0_1c9/1
+ATGGATTTCCCTCCATTGTGTGCATAGAGGTGTCCAAAAAGTGAGGCTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_90357627_90358090_2:0:0_1:0:0_1ca/1
+TAGCAACTTATATTCTCTCAGGCAATGGTTTCTTTTTTCTGTTTGAAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_184900782_184901265_1:0:0_1:0:0_1cb/1
+CGTTAGTTGAACAACACAAGCTTGTGTTTAGCTGCAAGATTAACATGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34520052_34520514_0:0:0_0:0:0_1cc/1
+TGTCCTGCTCCTGCTCCTGCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_121381246_121381739_0:0:0_0:0:0_1cd/1
+CTGTGTTCAGTACAATGCTATTTGTAATCCTTTAAATCCACCCCTTTGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_80355344_80355825_1:0:0_3:0:0_1ce/1
+ATATATCCTATCATATCATCTGCAAAAAAATGATATTTTAACTTCTTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_23025664_23026100_0:0:0_2:0:0_1cf/1
+GGCCCTCAGGATTCAACAGGTAGCGTGGCTGCTCAAACACTTTCTTAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_126877190_126877687_2:0:0_0:0:0_1d0/1
+GGACAGAGTGGGTTATGTTACAAGAAGCACTCAGACATTGAAATCGGAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_64317525_64318044_1:0:0_0:0:0_1d1/1
+TGTTTTTTTTCTTTTCTGTTGAGGGGTTGTTTCTTACCACAGGGAGTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_41387597_41388152_2:0:0_4:0:0_1d2/1
+AGCACTATGTCTGCGTAGATGCTGCCAAGCTCCTGGCTAGATGATAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_179273458_179273967_4:0:0_2:0:0_1d3/1
+GTCCTCCCTTCTTCGTAATTGTATCCTGTGGTTACATTTTTTTGCCTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_159718146_159718573_1:0:0_1:0:0_1d4/1
+AAAATGTCAACAATTGTTATCCGAAAGATTATTAATCTTTTTGCTACTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_77989741_77990190_3:0:0_2:0:0_1d5/1
+GCTCCTCCAATGGGGTCCGTGTTACTCATCCAATAGTGGATGACTGTGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_70921539_70922106_2:0:0_0:1:0_1d6/1
+ATATGCAAAATTTAAAACTGTTGATCTCATGGAACAAGTTGAATAATTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_135807545_135808030_2:1:0_0:0:0_1d7/1
+CAGAGCACAGTGTGCATACTGGGACCCCCATTTTGTGACCCAAGCCCAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_140999216_140999698_1:0:0_1:0:0_1d8/1
+AATGCTTCAATTAAATAACCAAAACCTAGGTTAGTCATTGAGGGTATCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148512883_148513388_0:0:0_1:0:0_1d9/1
+CTAAGAATACCCAAAATATAAGATACAATTTGTGAAATACATGAAACTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_95472009_95472435_1:0:0_0:0:0_1da/1
+TGTATATGTGTGTGTGTGTTTGTATGTGCATATGTGAAAGAGAGTGTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_19217196_19217734_0:0:0_1:0:0_1db/1
+ACTCAAGTGTATCAATGTATAAAGCTAGTACGTGAACCCTACACACACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_4075909_4076300_0:0:0_1:0:0_1dc/1
+ACTATGTTCATAGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_186978576_186979074_1:0:0_0:0:0_1dd/1
+CTGCAAATCGGGTGTTTGGATTGGATTGATGGTTCAGTGGTTAAGAGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_112188833_112189331_0:0:0_1:0:0_1de/1
+CAATTAATATTTATGAAAATTCATATTTATATATTGAAATGTAGTAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_173609986_173610514_0:0:0_0:0:0_1df/1
+ACAATCTGGGAGGTGAGTTGGCTCAGTGCCCTGACTGAAGTGACAAGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_22017871_22018438_0:0:0_2:0:0_1e0/1
+CCCCTAGCTTTCAAGTCTTGGGGTTGAATCCACTGTCTCCTGCGTGAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_48541209_48541729_1:0:0_2:0:0_1e1/1
+GGTCTGCAAACATAACTGAGTATCATTAATATTGTCAAGGACAGGTTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_10384181_10384617_2:0:0_0:0:0_1e2/1
+TTCCTGTTGTTTTTGTTGTTAAAGTTGGCATTCTGTTCTTGTGGCTGTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_20392227_20392827_2:0:0_0:0:0_1e3/1
+CACCAAGAGAAAACTTGTTCAGATACATTGATTTTTAGTAAGGATATGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_171278949_171279483_0:0:0_0:0:0_1e4/1
+TCCAAGCTGAACAAACCCACCGGTCCATATTGCTGGGGCTGCTGCTGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_58815142_58815652_3:0:0_0:0:0_1e5/1
+GGAGGAAGACATCCATGTAAAGGAGCAAAATTAAAGATGGGAATTGTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_157206264_157206747_1:0:0_3:0:0_1e6/1
+CATCCCCTAGTAAGAGTTATGATAAAATTACACTAAAGCTAGTTTTTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_130727486_130727887_0:0:0_1:0:0_1e7/1
+GGCAGGGTTTGGATATCTTTTCCCTACTGAGCAAGACAACAGCTTTGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56227774_56228368_1:0:0_2:0:0_1e8/1
+GAGGGCTTAGTGTTGATAACAACACTCTGCTAGCTCATTGGATAGAAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_163976865_163977422_1:0:0_2:0:0_1e9/1
+CCCCCCCCCGACAGATAACATACAGAATAAAAACTTGAACATGCCACACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_75768405_75768873_1:0:0_0:0:0_1ea/1
+AAACTGGGCTCAAGGATACCATGCGTTGCTTTATACCAACTTGGACCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_99777250_99777759_1:0:0_0:0:0_1eb/1
+TCAACTCTAGAGTCCTTCCTAAAAAAAGAAAATGAAAAAAAAAAAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_6944229_6944786_1:0:0_3:0:0_1ec/1
+GATCTAAAATTACCTAGAACATTACATGGAGATGTTGATTAAAGTCATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_6751099_6751639_3:0:0_0:0:0_1ed/1
+ATCCAAATAACTGTTCTCTTTCCATCATATGATACTGACACAGTGATCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_28492407_28492923_0:0:0_2:0:0_1ee/1
+TCTTAGAATGCTATGATTTCACATATCTCTGTATGTTGTAGTAGAAGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_25977449_25977911_3:0:0_0:0:0_1ef/1
+CAATACAATAATAATGTATCATTATAACAGTAGACAAAAGAAAGGAATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180012197_180012695_1:0:0_3:0:0_1f0/1
+GAGAACCGTGACTAATATAGAAGTTGGTACCAGGATAGGTTCTAGAGTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_139551031_139551593_1:0:0_0:0:0_1f1/1
+CATCAAGTCAAATTATAGCATTTTTAAAAAGAAACTTGATAGTATATGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_88565594_88566005_0:0:0_1:0:0_1f2/1
+TGTTCAGGCTAGAGTACCTGCATTAGCTCTTCCTTTCTCACACACACTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_28334498_28334996_0:0:0_0:0:0_1f3/1
+AGAGCTCCCTGAGACTAAACCACAATCAAAGAAATCACATGGTGGGACTC
++
+22222222222222222222222222222222222222222222222222
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq
new file mode 100644
index 00000000000..094a63da07d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-in6.fastq
@@ -0,0 +1,2000 @@
+@chr1_177668195_177668687_1:0:0_2:0:0_0/2
+GGCTGTTCTGTAACTCACTATGTAGACCAGGCTGGTATTCAACTCACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_102240227_102240757_1:0:0_0:0:0_1/2
+ATTGGGAGCCCTATGATCCATCCATTAGCTGACTGTGAGCATCCACTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_135092709_135093083_1:0:0_0:0:0_2/2
+TGTGTACTTGGTAGCAGACAAAGCTGAACTAGACCGTGGCATTAATTCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_173363751_173364238_0:0:0_1:0:0_3/2
+AGTTTCTTTTCCTTGTTATAGCTGTAAGGGATCTGTCTGTTTTTATCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_155990043_155990565_1:0:0_0:0:0_4/2
+CTTTCTATTTTTCTCAAATTAATTACAATCAAAAGTACTTCTGTAACGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_3703883_3704401_0:0:0_1:0:0_5/2
+CCAAGAAGTGGGAGTGGGTGGGTAGAGGAGTGGGAGGGAGGGTATGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148211558_148212105_1:0:0_2:0:0_6/2
+TGCCACACTGTTAAAGACATTTATCTTCCCTCTTGAACACCAATCCCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_30961675_30962138_2:0:0_0:0:0_7/2
+TTTCTGGTCCAGTCTATTTGGTTTTGTGTAGGCTTCTTGTATGATCATGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_86070681_86071151_1:0:0_0:0:0_8/2
+GTTTTATGATATCTTTACATATCCCATCTTTTAAAGTAGCCCTTCTATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_78259267_78259767_0:0:0_1:0:0_9/2
+AACAAAATCTGATGCACTTTTCTGGAGTATCTGAGGACAGCTACAGTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_143451378_143451824_2:0:0_1:0:0_a/2
+TTGATAAAAACTTCATGGTACTGGTATAGAGACATACAAGTAGACCAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163539961_163540475_1:0:0_1:0:0_b/2
+GAGGATGAATGAGTGACTTGAATTGGTGATTTTGAGGTCAAAATGTTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_70390520_70391012_0:0:0_1:0:0_c/2
+AATTTTAAACATCTTATTAACTGAGATCAAAGATATTGATTTTCTATTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_119090463_119090959_0:0:0_0:0:0_d/2
+AAATGTTCACTTTGAAATCACTTCAGACCTACAGGAAAGTTACAAAGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_12587911_12588392_1:0:0_2:0:0_e/2
+ATAATTTCACCTTTTGTCTCTGGGCGCTCATAAAAGATGCTATTGAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_21875665_21876102_0:0:0_1:0:0_f/2
+GGGGCAGAAGACCATGCCACATGAAAGGACCACTTACAGAGCTAGTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_22900274_22900767_0:0:0_0:0:0_10/2
+AATATATTTTAAAAATTCCCCATTGTGGTAGTGTAGACATAGGTCAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_97511239_97511754_1:0:0_0:0:0_11/2
+TGCACTAAATAAAGATAGAATATTAAAAGCAGTAAGGGAAGAAAGGTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_64669865_64670428_2:0:0_2:0:0_12/2
+CTTCTGGTTTTTCTGGCTTTCTACCCCGCAGAAAGTGATTTAGACTACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69102786_69103213_3:0:0_1:0:0_13/2
+ATTTAAATTACACAAAATGAATATTCGAAAAAAGGTACCAAGTTAGTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_117742994_117743506_1:0:0_4:0:0_14/2
+ACAGTCCAGTCTTCACTGACTGCTCCCCATCCCCTACCTCCTCCCCTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_53703453_53703930_0:0:0_1:0:0_15/2
+TTCAACAGAAACCTTTCAGCACGGCTCATGCTTGGGTTGGTTATGTAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17968135_17968661_2:0:0_0:0:0_16/2
+TAAATACAATACATGTTTGATTATGTGTGACTATTATCCATTAAATAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126734590_126735074_2:0:0_1:0:0_17/2
+GGGCAAATGCTTAATTCTTTTGCTCTTCTCGTTTGAAGTTCTTATTGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_15473022_15473574_0:0:0_2:0:0_18/2
+TCCTTCTAATTTCACGTTTTCTTTTTGTTTATAACACAGTGAGTTTCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32809503_32810008_3:0:0_4:0:0_19/2
+CAGGCAAGGCAACTGGAGCTGGAAGTTTAAACCTGCATGTTCATATTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101160086_101160574_0:0:0_2:0:0_1a/2
+AGCATTGGAAATGTAAATGAAGAAAATACCTAATCAAAAAATTTAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86845143_86845638_2:0:0_0:0:0_1b/2
+GGCTTTCCTTGTGGCACTGTCCAATGTCCCTTTAAGGCAAAAGCATGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_156394447_156394901_0:1:0_1:0:0_1c/2
+TTATGGCGAGATGAGCATCTCACTATAGAAATTAAAACTAATCAAAAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175220096_175220545_0:0:0_1:0:0_1d/2
+TCTCATTCAATAGCCTAGACTATTACTTTAAATACAATAAAATTTAATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_66136304_66136892_1:0:0_0:0:0_1e/2
+AAATGGTTTTAGAAGTCCTTATCCTGGGCTTGGATCTTCTCATACCTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_56699450_56700040_1:0:0_0:0:0_1f/2
+TCTTTTAAGTTGACAACTGAGTCTGAGCAGTGATGTTCAATGTATACTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_60449644_60450153_0:0:0_0:0:0_20/2
+GGGAACAGTAGCAGGAACAAGAGGGGTGGGGACAGATGCAGAAGTAGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_28286517_28287074_0:0:0_0:0:0_21/2
+CAATTTTTCTCAGCTTCTGACCAAATTGCTCTGCTTGGCCTCATACTAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_127946423_127946897_1:0:0_1:0:0_22/2
+AATCCTCTTTGTGTAAGAACAGCTGGTGCTGTTAACTTGTCATCTCTCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136274524_136275031_0:0:0_3:0:0_23/2
+GAGGGTGACTTGCTGAAGTCATTTCTCTCCTTTCACCATGTGGGTCCCCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_122372156_122372666_1:0:0_1:0:0_24/2
+GTTTCTGTGTGTCTGTATGTCTGTGAATGTGTGTGTGAGATTTTGTCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_19553027_19553520_1:0:0_0:0:0_25/2
+TTTGCGTATGGTGAAGTATGGGAGCCTTCTTACAACTGAAGAGGTGGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_57071218_57071658_1:0:0_0:0:0_26/2
+CTGTGACTTGGTAAACTCCATGGGGTATCTCCGTACAAGGTGAATGACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_7557012_7557560_0:0:0_2:1:0_27/2
+CAGATTTCCTGACAGTCAAGCTGCCTCTGCATCCCTGAGATCATGCTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18791508_18791966_0:0:0_0:0:0_28/2
+AAGCCAGAGTACGACTGCCCTTACATGAGCCCCATTCCCAATGAGCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_56244256_56244708_0:0:0_0:0:0_29/2
+ATGTTTCCATTTGCATTTAGCTAAAAATTGGCAAGAAGATTGTCATCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_30613322_30613773_2:0:0_1:0:0_2a/2
+GATTGCTTCCAGCTTCTCTCCAATTACTTAGATGTTGGCTACTGGTTTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_161898116_161898586_1:0:0_1:0:0_2b/2
+CACTAATTGAGAAATGCCTTACAGCTGGATCTCATGTAGGCATTTGCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_3742828_3743343_1:0:0_0:0:0_2c/2
+GTCTGGGAAGAACCCAACTGTGTTCTATTTAATCCTGCCCTCCTTCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_59624032_59624611_1:0:0_0:0:0_2d/2
+ATTTATTTATTTATTTATTTATTTATTTATTACACTGTAGCTGTCCTCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_98734890_98735381_1:0:0_2:0:0_2e/2
+AGTAGACACAGTGATTGTACAACAGGACATCTGATGGGACATTAGGACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_170863521_170863976_0:0:0_1:0:0_2f/2
+GTTTTGATTGTAGCCTTCTTCTTCACTTGTAGATGACTGCTTTCTTGCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_111611961_111612483_3:0:0_0:0:0_30/2
+CCCACCTGGGACAGACTAAATGATGCTTAGTTAACTCTAAAATTTCTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_125730124_125730581_1:0:0_1:1:0_31/2
+ATCGTTCCCACATCTTGCTTTCTTATTCCTCACACCCACAACCACAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_10873266_10873801_1:0:0_1:0:0_32/2
+TTCACTGTAGTTGTAACAAATGAGTTGTTTGTTGTGTTTTATAAAAACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175631956_175632547_3:0:0_1:0:0_33/2
+GCCGAGGATGCTATTTAAACATACAAGGTGTCTCATATGAGACTGGGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_20372115_20372592_0:0:0_2:0:0_34/2
+TGTCCTTCTTACCAGAATGGACAGATTGTGGAAACAGAAACATCTATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_172022589_172023145_0:0:0_2:0:0_35/2
+GCCAGGAAAGAGGAGGAAAAAAATAGTCTGACAATACTGCCCCAGCCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_168140019_168140474_0:0:0_1:0:0_36/2
+AGGGATCTGCACAAGTTTGCAGGTGTCTAAGTAGGTCAGAGGTATCAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_12207936_12208461_1:0:0_0:0:0_37/2
+TCATCTCAGACTTGCTATTACAATATCTAATCTTATCTTCTGATAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73438005_73438553_2:0:0_0:0:0_38/2
+TGGCGTGGAGGAAACACTGGTCTCCGTGGACGTCATTTGGCAGTTTTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_152770828_152771350_1:0:0_1:0:0_39/2
+CAGCTACAAGGAGGCACCCGGTCTCTAAAACAGCAAACCAACAAAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_23377131_23377643_1:0:0_1:0:0_3a/2
+ATTTTGTTTTTTTTTTAATCAACGGTAAATACACTGTGCATTATACCCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_101774130_101774651_1:0:0_0:0:0_3b/2
+GATCCAACAAAGATAGAGAACTTCAGACCAATTTCTCTTATGAATATCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_44505664_44506178_2:0:0_1:0:0_3c/2
+GCTGAGGGCCTGATTTTGCCTACTTTTGGACCCATAGGAACAATTTTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136585250_136585783_0:0:0_0:0:0_3d/2
+CTCAGATTGTCAGGTTTGTGGGACAAGTATTTTTTTTACCCACTGAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_125479421_125479942_1:0:0_1:0:0_3e/2
+GACAGGATAGAGGCAGCTAGTAAGCCATGAGGGCAGAGCTTGGGGGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_48288718_48289238_0:0:0_2:0:0_3f/2
+AAAAGATATAGACTAACAGACTGGCTAGACAAACAGGACGCAACATTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_162596088_162596584_0:0:0_1:0:0_40/2
+CAGGACAGCCACGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114964476_114965085_0:0:0_0:0:0_41/2
+ACTCACCATTTTAGTGAGTATACAAGACAAAAACTTGAATAGTCTAATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_132214583_132215104_0:0:0_1:0:0_42/2
+ATGGTGCCAGGGATCCAAACTCATGTTCTTATGTTTGCACAACCTTCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_4422836_4423410_1:0:0_1:0:0_43/2
+TTTTATCACCACAAATATAAGTGGGCCAGTGAGAATGATCAATCCATTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72831428_72831958_1:0:0_0:0:0_44/2
+AACAACAAAAAAAAAAAACCTGGGCTAGCAAGATGGCTCAGTAGGTAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17626572_17627059_2:0:0_0:0:0_45/2
+TTGAGGGAACACACATAGTAACCACCTACAGATAGGATAATTGGAAAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_122621502_122622050_0:0:0_1:0:0_46/2
+TAAACTAATTAATTATAATTTGAGGACAGGAGGGAATTACAGAACATACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_157981625_157982140_2:0:0_1:0:0_47/2
+GACGTCCTACATCCCTTCCAGGCTCAGCTGTTGGTTTTCCCTAGTTACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_86952334_86952916_0:0:0_1:0:0_48/2
+ATTTTGTCCTTCTCAATTTTTTTTCCTTTCTTTGGCTTTAACCTTGCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56589802_56590323_0:0:0_5:0:0_49/2
+CATTACGTGACGGCATTACCCCACAGTACCCACTTTGCTATGCTATTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_44959275_44959852_2:0:0_0:0:0_4a/2
+GGGCACCTGTCCTCCGGTCCAGACGGTGGCTGGCTGTCCCCTGCCCACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78655270_78655764_0:0:0_1:0:0_4b/2
+ATTATAGGTGCTTAGTGGGAAGCTTGATGACCTGAGTTCACCATGGGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_92742731_92743276_3:0:0_1:1:0_4c/2
+TGGGATGCTGAGGTGGGCGGGTATAAGGCAATGGAACTGGTCCATGGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133350357_133350894_2:0:0_0:0:0_4d/2
+GAGAGCGAGAGAAGGTAGAGAAGTAGAAGCCAGTCATTGCCATGCAGAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18383798_18384307_2:0:0_0:0:0_4e/2
+AGGGGGAAAGCCTGTGCTTTTTATTAAAGCATACCTACTGGCTTAGTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_94539200_94539737_1:0:0_1:0:0_4f/2
+AGTTTCAGCGAGAGACAGATAGATGAATGGAATAGAATTGAAGACCCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_131360576_131361118_1:1:0_0:0:0_50/2
+CGTTCCTTCCTACCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_55802170_55802665_0:0:0_1:0:0_51/2
+GAAATACTGCTTTCTCGAGCCTATTAATTATCTTGATATGAACTGAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_160986523_160987031_0:0:0_1:0:0_52/2
+TTGCATTACAAGTGTGAGCCTCTGCATCTGCTTCGCCTACTGTGCGCAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_10207724_10208191_1:0:0_1:0:0_53/2
+CCTGTTAATGGCCACCAGATGGGAGAGGTTCTGAAGAGATTTCCTTCCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_186877031_186877586_1:0:0_0:0:0_54/2
+TCTTGCGCGCGCTCGACTGGGAAGGAAGAACGACGCTGCAACAGGATCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_76761957_76762468_0:0:0_4:0:0_55/2
+TGTTTATAATAGCGAGACGCTTGAAAGAACCCAGCTGCCCCTCAACAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_117599116_117599626_3:0:0_1:0:0_56/2
+TGGCAACAGCAACAGTGAGTGTCTGTGGTGGCTGCATCTGGGATGGACCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_174656805_174657230_0:0:0_2:0:0_57/2
+ACCACACTGTGATTCACAAAGCTAGGAAGCGCTCTCTTAAGTTCTCCCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_31215276_31215715_1:0:0_3:0:0_58/2
+AATGCCTTCCTGGGACTCTGACCAATGGAGCTAATTCCAAAGACCATACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_126165616_126166084_1:0:0_0:0:0_59/2
+AGGATGAAGATTATATGTGAAAGAAGCACTTTGGTAGAGGAAGACTGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_164029809_164030262_1:0:0_2:0:0_5a/2
+TGTTGGGGTGTGGATAAAGTGTATATGAGTTGAAAGGTTGATTTGGTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_121717872_121718374_3:0:0_3:0:0_5b/2
+TATTCTCATGCAATAAACACAAAGCAAATGAAGCCAAAGCTGATGCTCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_160410719_160411215_0:0:0_1:0:0_5c/2
+AGTGTGCTTTTTGTACAAAATCAACAAATGATTTTAATATGATAGTATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100203985_100204499_0:0:0_1:0:0_5d/2
+GAAAGTCTTAGTTCCCATGTCTTACCAGCAGTCTAACTTGCCTTCTTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_177503365_177503816_3:0:0_0:0:0_5e/2
+ACAAGAGGTATGTCTTGGTCTGCCTTACACTGTTTACTTAAGCTGCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_164919242_164919704_1:0:0_1:0:0_5f/2
+CCCAAGCGGAGTAGACGGCAGGAAATAATCAAACTCAGGGGTGAAATCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_36958484_36958940_1:0:0_2:0:0_60/2
+ACCTTAGCCTCCTCCGAGCCGAAAGCCGCAAAGCAACTATTGTCTTTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_99520185_99520697_2:0:0_2:0:0_61/2
+CGACCTGTGATGGTTTGTATATCCTTGGCCCAGGGAGTGGCACCATCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_92584393_92584910_1:0:0_1:0:0_62/2
+AGCTACTGCTCTAACACTATATCTGTCTGCTTCCTGGCATGAAAATCGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_6665937_6666494_1:0:0_2:0:0_63/2
+TAATAATGATGTCAGCATTTCTTTCAGTGCCTCTAGGCCCTCTCTGACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_103781308_103781731_2:0:0_0:0:0_64/2
+ATATGTATCAAAGACAACTCGTCCCAAAAGAACCTTTCTAGTCCTCTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_35981688_35982179_0:0:0_1:0:0_65/2
+CCCTTCCTTGCTTCCTTCTGAAGAACCAGCTTGCCTCCATTTTAGGCTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_76873892_76874342_1:0:0_1:0:0_66/2
+TTCTGTAAGGCTGTGAATCACCCAATTTCTACATGTTTTCAGACCATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_148924276_148924708_1:0:0_0:0:0_67/2
+ACAAACCGTAGATCAACTTTATTACCTCCTTTATTATATTTAGAGGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_48352388_48352886_0:0:0_0:0:0_68/2
+AACATTTTACTATACCATTCAACCATCATTTGAGAAGTTTCCTCCTGCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_135109139_135109668_0:0:0_0:0:0_69/2
+CTGGCCAATGGAGATGCAGCCTATTGTCACAGACATGGTGACAGTGCACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133271389_133271883_0:0:0_0:0:0_6a/2
+CTAACCAAGTTACCCCGAGAAGGGCTGTGCTCTGGAGCGGGGAACTTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_143528403_143528953_0:0:0_3:0:0_6b/2
+AGTTTTATGAAACTCAGGTCAGCGATCCACACAGCACTTATCACAAGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_60739061_60739616_3:0:0_1:0:0_6c/2
+TTAAGGAATAGTGATTTTTGTTTCCTGTTATTTTTGTTATTAGAGGTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86239673_86240187_2:0:0_0:0:0_6d/2
+ATGCGTGATTCTAAGGCTGGGCCGCTTGTCCTGAACTGTGTGTGCTGCGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_8425683_8426176_2:0:0_1:0:0_6e/2
+CTTGCTGTGTTTTCGTAGTCTTATACTTTGTGGGAACTAATCCACTGTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34934564_34935093_3:0:0_0:0:0_6f/2
+ATTTATTCATGTATGCTTGAGTATTCATGTAGTAAAGAGAAGACAGCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_43897170_43897709_4:0:0_1:0:0_70/2
+GATAAGGTCACAGTCTGTCAGTGATGCACAGGACAAATCCAAAACCCGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_64512455_64512956_0:0:0_0:0:0_71/2
+AAAGTCAGGAGAGGCTGAAAGCTAGGCCTCTTGTACCAAGCCACTAAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72637152_72637620_2:0:0_2:0:0_72/2
+ATGCCAGTGCACTAACACAAAGCCTGGCATGGTAAGGGACATGCTCGTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_149528405_149528902_2:0:0_0:0:0_73/2
+GTGAAATGATAGACACCAACCCGCTTAAAAAAACTTTCCACCCCAAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_89951120_89951611_2:0:0_1:0:0_74/2
+CCTCGAGGTCGACTCCTCTAGCCCTGCATGGGATATGAGTCGTCCCCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108291981_108292457_1:0:0_1:0:0_75/2
+TTTTGGTTTGTTGAGGGATTACTTTCTTGATTGTTCTAGGGCGTGATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130354891_130355474_0:1:0_0:0:0_76/2
+GATGTGCACAAACATAAAAAACACACACACATGCACACACAAAAAAAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_166207187_166207634_1:0:0_3:1:0_77/2
+CTGAAGTCAGGCCTGGAACTCAAGCAGGACAGGATGCAGGCACAGATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_178111549_178112035_3:0:0_3:0:0_78/2
+TGGACACAAAACATTGAGAATGAGATTGCAACAGGATTCTGTACTACAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_64705135_64705653_1:0:0_3:0:0_79/2
+AATGTACAGTGGGCTTGATATGAAAATATTACAACATATAATTAGATCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_50237028_50237524_0:0:0_2:0:0_7a/2
+TGCAGCTTCTGGGTATTATAAATAAGCCTGCTATGAACATAGTGGAGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_134752385_134752911_2:0:0_0:0:0_7b/2
+CATTCTCTCCTTTGTCTGGCAGTGCCACAGCACAGGGTGCCGTGAGAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_168207741_168208312_2:0:0_0:0:0_7c/2
+GAATGACCCGAGATGTGAGGACTAGGCAGGTTGCTGGGAGGAGGCCATGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_151034392_151034882_0:0:0_0:0:0_7d/2
+ATTAAAGACTTTACAAAAACTAACCTCATGAAACTGAAAAGCTTCTGTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_149618965_149619431_0:0:0_1:0:0_7e/2
+TTAGGTCCCAACACTCACTAAAAAGACAAGGTTTTCCCGCCGTTCTCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_72479618_72480144_1:1:0_0:0:0_7f/2
+GGTGCCAACCACTGTCAAGCTAATAGCAGACTAAAAGTTTTACCGGAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_18771436_18771929_1:0:0_2:0:0_80/2
+TAGTTTTCCAGTGAGGGCTAATAGAACAAAGTGGTATAAATGGTTCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626454_177626877_2:0:0_1:0:0_81/2
+GGTGGTGCAAAGAGAGTCCTGAAGCTGCAGATAGAGTGACAAGAGAAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_58671914_58672334_4:0:0_0:0:0_82/2
+ATTCTTGTGTGACCACGCCCCTAGGATCCTGGGATCCTGGGTGTGTTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_123634655_123635138_1:0:0_1:0:0_83/2
+TCATCCAGAGGTCTGGAATCTTGTTCACAGCACCCATATCTAGCAGCCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_32777949_32778514_0:0:0_2:0:0_84/2
+ATTTCCAAAAATTAAACTTGATCTTCATATTAACTTTCTAATCTACAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321026_38321532_2:0:0_2:0:0_85/2
+TTGCTTACATTCATGGTAGGCCTAACACCACCCAGCATCCTTTGCTTCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_31837668_31838221_1:0:0_2:0:0_86/2
+CCTGGTGTCATTAGCAGAGCCTGGTGGTTTCTGGATTTAACTGGCATTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_189752778_189753180_2:0:0_0:0:0_87/2
+AAGAGAGAGAGAGAGAGATAGCGAGAGAGAGAGAGAGAAAGACAGACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_43602264_43602720_2:0:0_0:0:0_88/2
+TTGTCTTGAGCTGATGATGACATGAGACATTATCCATCTCCAAAATGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_29558267_29558774_2:0:0_0:0:0_89/2
+AATTAGAAAGGGCAATCTGCAAATTCATGTGGAATAACAAAAAACCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_59048796_59049203_1:0:0_0:0:0_8a/2
+TCTGGAACTATAGGACTAAACTTGATTGGCTGATGCTAGGGAGCAGCTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_31285666_31286194_0:0:0_1:0:0_8b/2
+AAACAAAACAAAACAAAACAGATTCAATCATGTTAAGAGGGATAACCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159055630_159056144_1:0:0_3:0:0_8c/2
+GCTCTCTCTAGGAAGGCTCCTTGTTGCCAGACGTCATCCTCTCATTCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163934531_163935036_0:0:0_1:0:0_8d/2
+CAAAGGCTTACCTAAAACAAGCAGTATATGACAGCTAGCTGAAATAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_116610918_116611481_1:0:0_0:0:0_8e/2
+ACTTAGAATTCTAAATAAAAGGTTAACTGTTTTCTTGGAATGCACTTAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_141208156_141208756_0:0:0_0:0:0_8f/2
+CTGAGTTATGCAGCCTTGCAGAAAGTTCTGGACAGGGTTACTTTTCAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_45492268_45492792_1:0:0_3:0:0_90/2
+AGTACATTAGCAGCCTCTGGAGAAAGAAGATATGCTGCAGTTTGGAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11755179_11755683_0:0:0_1:0:0_91/2
+GGGCTCCCACAAATATTCTAGTATGCTTTGCTCTAGGATAAATAGAATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156738022_156738530_2:0:0_2:0:0_92/2
+GATGCAGTATAAATGGTGTAGCAGATGCCCGAGACCTCAAACACACCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_95480426_95480839_0:0:0_0:0:0_93/2
+TTAAGTGATGTAACTGGATAACAGTAATGAAATTTTAGGTTCTCAGTGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_173460574_173461156_3:0:0_1:0:0_94/2
+TAAATACCAAAAAATGGATTTTGTCAAATAAGGTCTTATAATACCACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17445381_17445808_2:0:0_4:0:0_95/2
+TAGAAACTGGCAGCCTTTAATTGTCTTGTAGCTTTACCTCTTTGTATGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_76540003_76540477_2:0:0_2:0:0_96/2
+GTGTAGCTCATATGTGACAGCAAACATTGTCCTTGCTGTAACTTTTAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_12896019_12896500_1:0:0_1:0:0_97/2
+ATCCCAGGAGCTTGGTCACACCAGGTTCTCAGGATCACAGAGGCAGCTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_41708628_41709145_0:0:0_1:0:0_98/2
+TACATGTGTGTATATGTGTGCATGGTGTGTACGGTGTGTATGTATGTGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_106826115_106826660_0:0:0_1:0:0_99/2
+TGTCTCATTTATGGGTCTTTAATTCTATTTTATTGATTGACATGTCTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_13247654_13248181_1:0:0_0:0:0_9a/2
+ATCTGCAGACAGTTCTAACATCTGATGTTCATTTACTACAGACCAGTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117777350_117777861_0:0:0_1:0:0_9b/2
+AAATGTACTCACTGATAAGTGGATATTAACCCAGAAACTTAGTATAGCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77191506_77192008_2:0:0_1:0:0_9c/2
+TAAAAAAAAAAACTCTTTAGTTTGGCTTGCATGTGATTCAAGGTTTCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36849743_36850269_1:0:0_1:0:0_9d/2
+TCTTTCTAGAACAGACTCCAGTTCAATAACCATTTATTGGTTGGGTGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_148890840_148891366_0:0:0_0:0:0_9e/2
+AATCTAAAATTTGAACCCCTTATACCCTTCAAATCCACCATCAACTGTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_84671373_84671880_2:0:0_1:0:0_9f/2
+TTCTAGGGACATTCTTTTCTTTCTACAGATTTCGATAATTAAAGGAGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102434771_102435253_0:0:0_1:0:0_a0/2
+ACTTCCTCTTGGTTAGTTGTCCAGTGAGTTCTACATTGGTCTGTCTCTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_100209819_100210321_0:0:0_1:0:0_a1/2
+TCTAAATGGGATGTGGCTAAGCTGGCAGTTTGCTGGCTTAGCATTTATGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_62044005_62044573_2:0:0_1:0:0_a2/2
+GTCAGACATCAGCATCACAAATGCAGAATGACAGAAATTGACTTGCACCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_85132332_85132871_1:0:0_3:0:0_a3/2
+CAAAAGAAAACATTTAATTGGGGCTTTTTTACAGTTTCAAAAAATAGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58843215_58843696_0:0:0_0:0:0_a4/2
+CGTGCCAGAAGAAGAGAGTGACTCCTCTGGAACTGGAGATACAGGCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_137975188_137975732_1:0:0_1:1:0_a5/2
+TGGCCAGATACAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_141967561_141968074_0:0:0_0:0:0_a6/2
+TCAACATATATGACATCCATAAATCAATGATTTGACTATGAAACCATGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8624607_8625140_1:0:0_1:0:0_a7/2
+TTAACTTTCAAGACAAGTGAATACTATATGATTTGGTGATTCTATGCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_138783244_138783650_1:0:0_1:0:0_a8/2
+GATACTCATGTGTGTGCCCAGCGGCTCTTTGAAGCTTACGTTCTTACATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_52699200_52699639_1:0:0_1:0:0_a9/2
+TCGCCACCGTCTGCTGTCACCTGAATTTTTGATCTTAGCCCTTCTGACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_32849205_32849709_0:0:0_0:0:0_aa/2
+AAGTCAGAGGAAGCAGCCAGAATTAGCTGGAGCACCATGAGAAGCACCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_182043596_182044137_0:0:0_0:0:0_ab/2
+AAAGAAAAGAAAAGAAAAGAAAAGAAAAAATGGACAAGAAGGCAAATAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136004325_136004842_4:0:0_0:0:0_ac/2
+AATCAGCTAGTTGGTTTGTCAGAGGAACTCTCAAGAGAAGATAGCACTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_174545541_174546018_2:0:0_1:0:0_ad/2
+TGTCTGAGGCATTCTGCAGAGCTGCGTTACTTTGTTTTGTTGAAAGGTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11117502_11117925_0:0:0_1:0:0_ae/2
+CACTGCATATACTATTGACCTAGTCTGACATAATACCTCACTTTCCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_44177515_44177974_0:0:0_3:0:0_af/2
+CTCAAGAAGAACTAAACCCACACAGAAGTACCTTGGTCAATATTTCACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72645507_72646002_0:0:0_0:0:0_b0/2
+AGCCCCAATGAAATATTTCATGATGTTTCTTTACAGGAATAGAAACCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_147283777_147284272_0:0:0_1:0:0_b1/2
+TGCTCCCTTTTATTTTTGTTGTTAGAGTTGGGATTCTGTTCTTGTGGCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_133675964_133676447_1:0:0_0:0:0_b2/2
+CATGTCAATGTGTGGGTCTGTTTGTAGGTATGTGCCTGAGCGAGCAAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_114568587_114569130_0:0:0_0:0:0_b3/2
+TCCGAGTTGGGGTTTACTATTCTTATTTGTTTAGTAAGATATTAAAGGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_111695385_111695895_0:0:0_0:0:0_b4/2
+TGATTTTCTCATCCGTAGATGAGTGGGCTTTTAACCTTGGCTTGGGTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_172273320_172273788_1:0:0_0:0:0_b5/2
+AAGAAAACACTATTCCATAGGAACCTGAAGCCAGCTTCCCGTCTCAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29014340_29014871_0:0:0_2:0:0_b6/2
+GCAAGGCTCCATCTCCTACTAGCACCACTCCCTATGGGCCAAGTATTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626521_177627066_1:1:0_0:0:0_b7/2
+GACCGGCACCTCTCACTGTGACCATTTTGAGTTTCTTGCTCTAAACTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_110742845_110743354_1:0:0_0:0:0_b8/2
+CATCCAATAGATGACTGAGCATCCACTTCTGTATTTGCCAGGTACTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14101155_14101687_3:0:0_0:0:0_b9/2
+CTAAGGTAAATTAGATCTTCCACCTTTGATTTACCCAGTTCTCCCAAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_38147934_38148475_0:0:0_0:0:0_ba/2
+TCCATCTGGAGTATTCAGAGGGCCCTTGAGGTTTGATGCTCATCCACGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_84834550_84834957_2:0:0_1:0:0_bb/2
+AGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGCTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_94046734_94047311_0:2:0_1:0:0_bc/2
+CTGTGGAACAGGAAGTCGAAAATTCTAATCAGGATTCTCTTGGTTAAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138724568_138725155_1:0:0_2:0:0_bd/2
+GATCTTCCCTTGGCTCAGCATTATTAAGGAAGGTGCTGGCTGAACCAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_105672406_105672966_0:0:0_1:0:0_be/2
+TCAATTACTACCATTTTGTGCATATTTTAAAAGCACACTATGGACACACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_157814995_157815529_0:0:0_3:0:0_bf/2
+TGACATACAAGTAATAAAGCCAAATACTTAAATAGGCCATCTCTGTTACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130059190_130059641_1:0:0_0:0:0_c0/2
+GTTGGGGGTTGGGGAAATCTTTAGGAAGTTCCAGAGACCTGAGACAGGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18604367_18604942_1:0:0_0:0:0_c1/2
+TAGCGGTACACTGTGTGAGCTCTAGGAAAATACAGAGCTCAGGAGATTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_160029930_160030407_0:0:0_1:0:0_c2/2
+CAGATAGCTAGCTTATGGACTAAGATTTTTTTTTAGAGTGGCTTAGTACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32417120_32417575_0:0:0_3:0:0_c3/2
+AGTTATACATGTTGTGGTGGACCCCAGCAACAAAATTACTTCCATTCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_91572336_91572825_0:0:0_3:0:0_c4/2
+CACCTTCAGGAACTGTTAGAGGTGGTTCCTGTTGCTCTTACGCCCCCCGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_167308006_167308522_0:0:0_0:0:0_c5/2
+GCCCGATCGCCTACCTCACACTAGAACCCTGTCACACGGTGGCTGGACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53658226_53658697_1:0:0_1:0:0_c6/2
+GTTCTTTTGTAATTGCGTTACCTCACTCAGGATAATGCCCTCCATGTCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75542501_75543075_2:0:0_0:0:0_c7/2
+AAGTTCTCTCTCGCCAAGGTAGAAGCTAGAAAAATGCATATGTCCTGACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_49392954_49393517_0:0:0_2:0:0_c8/2
+GTATCTTTTTCTCTCCTTTTCATTTTTTAAAGTTTATTGTTGTTCTTAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18890524_18891056_1:0:0_0:0:0_c9/2
+AGTTGATTCCGGACTCTTCAGAGTCCAGCTTTTTGGGGGTTTTGTTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_13661516_13661931_1:0:0_1:0:0_ca/2
+AAAAGGAGTAGGCTAAGGTAGTGAATACACTCTACATCTCTATTGTGGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69507936_69508419_2:0:0_1:0:0_cb/2
+CACCTCGAGAAAGAGCCAACCATAGAGCATGTGTGTTGATTGTTTAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_171186227_171186672_2:0:0_1:0:0_cc/2
+CCCTTCTCTCTTCTAGAAACCAGACAATCCGTCCTTATACTCTCTAGTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_151167139_151167658_0:0:0_3:0:0_cd/2
+TCCAAATTAGACAGACTTCCTCTTCCTGTGGCCTGGACTGTTTTTTCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_166490443_166490901_1:0:0_2:0:0_ce/2
+GATGTCAGAAACATGATAGGTCTCAGAATGTGAGGATTTTAATCCCAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78053476_78053981_1:0:0_0:0:0_cf/2
+ATAGCATATCCCCTTAGCCAGAGAGCTTAGACTGGAGAAGCACAGCTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_27573317_27573793_0:0:0_2:0:0_d0/2
+TTTAAGCTTATATAATAAAAAACATAATTACAAATCTATACAAAAGTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_74520986_74521432_1:0:0_4:0:0_d1/2
+TTTCCTTATAAAGTCTGAGAGTTTAGTTAGTGCTGACTTGTCAGAAACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_194568812_194569255_1:0:0_0:0:0_d2/2
+AAGTACCATCTGTATTAATGATTCACAGTTATTTAAATATTTGAACAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173094678_173095086_1:0:0_0:0:0_d3/2
+TAAGGTTGAGTTTCTGATAGGATACCATGAGGTAAAGATTTCCAAGCAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_125473775_125474200_1:0:0_0:0:0_d4/2
+GCAGCTTGACTCCGGTTGTGATTAATCAAAAGAGGTGACCCTGGGAGACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_60312834_60313394_2:0:0_1:0:0_d5/2
+GAAGGAACGGGAAGGAGAAATGGTGTAATTAAATTATAATCTCAAAAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_21769340_21769783_1:0:0_1:0:0_d6/2
+GGCTAAGATCAAAACTTCAGGTGACCGCAGATGCTGGCGAGGATGTGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_29011734_29012196_0:0:0_0:0:0_d7/2
+AATCAGATTTTGTGTTTTGTTTGGTTTTCCATTAATGCTTTCACAACGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_55988735_55989188_1:0:0_0:0:0_d8/2
+AAGATTAGTTCTAAAGACATTACAGCTGCCACTCCAAGTTCTTGCCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_143689772_143690244_0:0:0_2:0:0_d9/2
+TCTAGTTAATTAACACTGTTATTACTTTACATGTTGCTCCATTTTGTGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102292799_102293241_0:0:0_2:0:0_da/2
+GAATACGATTACTAATTCGTTGAGAAGGTGATATGGCCATTCACAAAACG
++
+22222222222222222222222222222222222222222222222222
+@chr1_175815890_175816392_0:0:0_1:0:0_db/2
+AACATTTCAACCTCTCCATGGCACTGAAGTTTTAATCAGCCAATCAGGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_65030887_65031423_1:0:0_0:0:0_dc/2
+TAATGTTATTCCTGAGATTTTTCCAGAGAAACAAATCCCACCATTTTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_77446136_77446727_1:0:0_0:0:0_dd/2
+GGACTACTTTCACTAAAGTGGAAAAACTCAATGGTGCTGTGAAACCTCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_79825884_79826306_1:0:0_0:0:0_de/2
+CAGGGGAACACCAGGGCCAAAAAGGGGGAGTGGGTGGGCAGGGGAGTGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_142137580_142138145_0:0:0_1:0:0_df/2
+GCCTCTAACAGTACCAAGGCTAAGCTGTTCACTATGACTTCATACCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77524851_77525306_1:0:0_2:0:0_e0/2
+GCAAGCTCCCGAAATCACAAGTTTGCAGACCAGGCAATGGGAAATTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26694201_26694676_0:0:0_0:0:0_e1/2
+ACAATCGAATCATTATCTAGATATTTTGATTATCTTTGCTTTAGGTTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_93157579_93158060_0:0:0_1:0:0_e2/2
+CCTTTGGGATTCTCCATCCAATGAGCCTCAGTTTCCTTACGAGAGGGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_93554302_93554745_0:0:0_1:0:0_e3/2
+ACAGGATGCAGCTGGAGACTTCAACACCTTACCTCCAATAATAGTCATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_115859373_115859816_1:0:0_1:0:0_e4/2
+GCATGCATCAAAGCAATGGTCCCTTAAAGCAGAGGAGTCAAGACTTTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_59908209_59908731_3:0:0_0:0:0_e5/2
+CTTGTTGTCTAAAAGGACTGAAAGGCAAGATTGGCTGCTGAGGTACTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_154628329_154628794_2:0:0_1:0:0_e6/2
+TGTACAGACACTTTATAGGTGTCTTTGGTGACTTTGGTGACACTCTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38934187_38934653_1:0:0_1:0:1_e7/2
+TTATAGCTTGCAATAGAAAATGGAGTTTTGTTTTTGCCAAATAAATGGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176440703_176441215_3:0:0_1:0:0_e8/2
+GGACCGAGCCAGTCTAGATATTGCAGAACTAAGAGTGTGTCTGTGAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_146248574_146249007_1:0:0_0:0:0_e9/2
+GAATAGATTGTACAGAATCAATAACCTACCAAGCATTTGCCTAGGGACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_137417062_137417534_1:0:0_0:0:0_ea/2
+ATGCCCAGTCACCCACAGTTGGTCTCCTGTCTCAGCCCCAATAACTAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_55607180_55607772_1:0:0_0:0:0_eb/2
+GGCACATCATTATCCATTGGTAAGCTTTGCTTTTTCCACAAGGTCACTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_174928179_174928755_0:0:0_1:0:0_ec/2
+AATTGCAAATAATTTTTATCCCATTTTGTATGTATGATAACTGATACCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_113923154_113923648_3:0:0_1:0:0_ed/2
+TAATGTGAGGTTACCTCTGGCACTGAGGACTATTAAGTGGCTTTAAATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78423064_78423594_1:0:0_0:0:0_ee/2
+AACTTGATATATGTTACTGTGGACCAAATGCCCTTCCTTCTCCAGTATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_154582561_154583019_0:0:0_1:0:0_ef/2
+CAGCAGCCTTGTTTGTAGTCTTATTATGAATTCAACAATATGTCACATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_181723357_181723842_1:0:0_2:0:0_f0/2
+CATGGCCATTTTCAAGACTCAGGTTGTGGACATCACACTAAGTGAGATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176206787_176207249_1:0:0_1:0:0_f1/2
+TGTGACAGTCTCTGGTGGCCTTACACTCCTCCTCTTTTTGCCTCTATGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156026308_156026788_0:1:0_2:0:0_f2/2
+ATTTTATTTTCAAAGCACTAAATTATTAGAATATTTTACCTTTTTATATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_55128175_55128671_1:0:0_0:0:0_f3/2
+CAGAGCAGTGAGCGAGTTTCCTGGAGAGGCCCGTGAGGGGACAGTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_184447109_184447646_1:0:0_1:1:0_f4/2
+GTTATATAACCTCATAGCAGTCACCAAATGAAATAAGACATTCCTCGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_194617734_194618226_0:0:0_0:0:0_f5/2
+GTGATTCTCACATTTATTCTTCCTCTATTATTGTTTATGTCTGCATGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_80810218_80810755_0:0:0_0:0:0_f6/2
+AGAGAAAGGCAGAGAAATAGAAGAGAGAGAGAGACCTACCTCTGATAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_144296368_144296930_2:0:0_2:0:0_f7/2
+ATAGTTCCTTTTGACATAGATCCTTCTAAAGGAATTGTAAGGGAATGTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108312503_108312946_1:0:0_2:0:0_f8/2
+GTTAAACAAGCATGCAATCCCACCAACAATGTAGGAGTGTTCCCCTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_78228179_78228640_0:1:0_0:0:0_f9/2
+CTGAGTCTTGTTTGAGGATGGATGAACTGATATAAACGTTTTCAAAAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_52088998_52089426_1:0:0_1:0:0_fa/2
+CTGTCCTGTCTTCCCTCTCCTCCGATCCCTCTTCTGAGTACTGAGCTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_30782403_30782942_1:0:0_0:0:0_fb/2
+AATATATTCACCTACACCTGTTAACTCAAAGGATCTGCTTCAATACTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_6435675_6436268_3:0:0_2:0:0_fc/2
+GACTCATTCATTCCCAGAGAGGAACAAAGGAAAATACCACAGGCATTTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_164237997_164238538_0:0:0_0:0:0_fd/2
+CATCAGACAGACTTCCAGATAAAACGGGTTTCAGATGAGATCAGTACTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_187097969_187098475_2:0:0_2:0:0_fe/2
+CCATAGCAGCTGTGTGGAAGTCATGACTCCTGGAGGTCAAGTGACTATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44694856_44695375_3:0:0_1:1:0_ff/2
+TTCCATAATATCTCTTACTATCAATGGACTCAATTCGCCAATAAAAAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_111782668_111783223_1:0:0_3:0:0_100/2
+GCTCTATCCCGTGGATGGCTGTGAGCATCCCCTTCTATTTGTCAGGCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_94206847_94207360_1:0:0_1:0:0_101/2
+AAGCAAAACTGAGAAGCGGCAAGGAGGAGAGAACAGAATGGAACATCACG
++
+22222222222222222222222222222222222222222222222222
+@chr1_132119789_132120286_3:0:0_1:0:0_102/2
+GGCAGGTAGGCGGCGGGCGGACAGGCCGGGCAGCTCAGTGAACTCATATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_34226734_34227203_0:0:0_0:0:0_103/2
+AGCGGGCTACTGATAGCCCACAGGTTCAAACCAGACAAAATCACAGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_138105716_138106319_4:0:0_1:0:0_104/2
+ATAAACAATCATGGCTCCTTAATTAACACAAATACTTTGAGGTCTCAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_126030856_126031342_1:0:0_2:0:0_105/2
+CAATTGTTGTAGAAACATTTCAAGAAAAGCGTGTATACAATTCACTAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_118807485_118808058_0:0:0_1:0:0_106/2
+TTCCGAAAAAGAAATAAGCAGAAAGCTGTTTGACTTTTCCTGGGGTGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_19849114_19849606_2:0:0_0:0:0_107/2
+TTCCTTAGGGTGCTGTGGTGAAGGTCTTTTATGACAGCAAATGGCAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_66877733_66878136_2:0:0_1:0:0_108/2
+GAGCATCATAATGGCCCATCGGTATCAAAGCTAAGACACGAGCATGGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132522495_132522987_0:0:0_1:0:0_109/2
+GCCCTGACTAGTGTAATAGGCCACAAGACGAAATGGAGCCTAGATTCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117050436_117050942_0:0:0_1:0:0_10a/2
+ACCCAATCACAAAAGAATACACATGATGCGCCCTCACTGATAATCGGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_125967212_125967705_0:0:0_0:0:0_10b/2
+TCAGGGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69313718_69314189_1:0:0_2:0:0_10c/2
+TTTTCGTAGATGACACTATCACCTCTGCGTATCTGACCTCATCCTCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_60897368_60897871_1:0:0_1:0:0_10d/2
+TTCTCTAGCTTCTCCATTGGGGGCCCTGTGTTCCATCCTATAGATGGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_174325015_174325549_0:1:0_2:0:0_10e/2
+TTAGAAATAACTTCAGAATGTCTTTTTGCCCCGTACAAATAAATAAGCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_85055965_85056468_2:0:0_0:0:0_10f/2
+CATAGAGAACATCGGCACAACAATCAAAGAAAATGGAAAATGCAAAAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_131415777_131416249_5:0:0_1:0:0_110/2
+TTTTGATCTCCTAACCAAAGGAAGATCTCCCAGTTTCATTGGTTCCAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67136277_67136702_3:0:0_0:0:0_111/2
+GTGCCATTCTGCTTTACTCAAGTGTTCTCCGTTTTACAATTCAGGAAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8402131_8402528_1:0:0_2:0:0_112/2
+TAGTTCTTATTACCATTTGGTTGATTTCACCCCTGATTTTGATTATTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_155126875_155127345_1:0:0_3:0:0_113/2
+TTGGCCAGCGTGAGATACATGCGACCCTGTTTAAAAAAAAAAAATCAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_93916438_93916928_0:0:0_0:0:0_114/2
+GGCAGTGATGTCTGAGGAGGACTCTTTGGGCAGATCTGAGGCCTGCTCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_135734641_135735118_0:0:0_0:0:0_115/2
+GTTGGGCAACCAGTTCATAGCACCACAGCTGTAGGAGGCAGAACTGGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44391025_44391499_0:0:0_1:0:0_116/2
+TTAGCCAAATTAGAGGGTCGTCTTGAGGCACCTCAGAGACCAGAGTCTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_110722550_110723095_2:0:0_4:0:0_117/2
+ATATAGTAAAATATATCATTGTTTGTATCTAAGCCATTATATAGATACGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_185586471_185586808_1:0:0_0:0:0_118/2
+GCTTTCTGGTCTGATTTGACTCTTAGCGAAGGTAAATGTTCACGCACCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_182936908_182937483_1:0:0_2:0:0_119/2
+CAAGCAGACACATTCATGAGGATTCTATCTGATTCTTCAACTTTTATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_136882207_136882635_0:0:0_2:0:0_11a/2
+GTTTGGTATTTGAAAATAATGTCTGTGTAATGGATTATGAGAACGGACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22027558_22028086_0:0:0_2:0:0_11b/2
+CCCTGGAAGCTCTGTGGAGTCTGGTTGGTTGATATTGTTGTTTTTCCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101069088_101069523_0:0:0_0:0:0_11c/2
+CTCCAGCTTGTTTCTTCAGACCTTTTGCTTGGAAAATTGTTTTCCAGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133430180_133430643_0:0:0_3:0:0_11d/2
+CCTGAGATCCTGTCACTTGATCTGAAGTTTTGCCTTCTGTCTCCCCTGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_141505317_141505766_0:0:0_2:0:0_11e/2
+TTATATGCCCCAGTACAGGGGAACACCAGGGTCAAAAATTGGGAATGGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103387516_103388014_1:0:0_1:0:0_11f/2
+ATGATTTCCCTACCTGATGAAGGCTTACTTCTTTCTTCACCTTATTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_134753416_134753860_0:0:0_1:0:0_120/2
+GGACCTGGGCTTAGGGGACAGCAGCAGTCTGACCTCGGCAACAGGGAGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_168048225_168048764_3:0:0_0:0:0_121/2
+CTATCATGATCACATTACCCTTACATCACCATCATCACGAGCCCATCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_15110325_15110842_0:0:0_1:0:0_122/2
+TATGGTTGTATTAAAGTTGACTAATATTAAGAGCTTAAATAGATTTAAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_71511848_71512298_1:0:0_1:0:0_123/2
+GCTTATTAATCCTCTTCTCTTCTTGTATAAAGGGTGGGAAGTAGGTGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_37275066_37275622_2:0:0_0:0:0_124/2
+GCTGGTTTCCAAATCACAGAGACCTCTCCTGCCTCTACTTCCTGAATCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191970326_191970894_1:0:0_0:0:0_125/2
+TCGTTAAGAGTAACCAGGGCTCTTAACTGCTGAGCCATCTCTTAGACTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_137258018_137258449_1:0:0_1:0:0_126/2
+TATTGTGAAGTGTTATGTCTGATTGGCTTTTTCTCTTCTTCGGTGAGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_163885263_163885763_1:0:0_0:0:0_127/2
+TGCAAACCCTTTCAGCTCCTTGGGTACATTCTCTAGCTCCTTCATTGGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_95122061_95122611_1:0:0_2:0:0_128/2
+ATCATCATAGGTGGGCAAAGGAAAGTGTGAAATAGTATAATTTCATGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191245641_191246131_1:0:0_1:0:0_129/2
+TTCTTGAGAGAGGCCAGGCTTTGGGGAACAGATGTCGCACAGCACTAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_11721955_11722368_1:0:0_3:0:0_12a/2
+GGGTTGGAGATCCCTTTAGCTCCTTGGGTGGTTTCCCTAGCACCTCCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102954712_102955237_1:0:0_1:0:0_12b/2
+AAGTGGTGTAACCCAATCACAAAAGTACATACAGGATATACACTCACTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_26914346_26914925_0:0:0_1:0:0_12c/2
+AAGGGGAAAAAAAACCCTGCATCTGATATGCAAAGACCAGTCAGAATAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_151053369_151053909_1:0:0_0:0:0_12d/2
+TCTTCTGTCTTGAAAAAGAAAAAGAACACACCACACCCACACACCACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93621447_93621970_1:1:0_1:0:0_12e/2
+CATTAAGTGTTAGTTTTAATAGCGCATTGAAAACCCTACCATTTCAATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_13530953_13531445_0:0:0_0:0:0_12f/2
+GAGTTCATTAGTACATTGGTTGTTTGGAACACAGAAAATCTTTCCCCATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_154530120_154530631_2:0:0_4:0:0_130/2
+AGGCTTTACTTAATCCAAAGCATAAGTACATTGTTTGACACCCTGCAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_100109085_100109588_0:0:0_2:0:0_131/2
+TCACAGAGGACACTCACAGAGATGAACCATGCTCCCAGGGACAAGATGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_150348101_150348543_0:0:0_0:0:0_132/2
+ATTAAACCTGCTGAGTTATTTGAATTCCAGAGACTTACATAATAAACTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8725925_8726392_0:0:0_3:1:0_133/2
+TATTCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_189147844_189148204_2:0:0_1:0:0_134/2
+TTAAGACATATTAATTTTAGGAAGTAAAAATAAATTCATTTAAATTGGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_45618673_45619149_2:0:0_2:0:0_135/2
+CTGGATGTCGCTTGTGCAGATCTTGAAAATTTTGTCATAATTGCTGGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_104062147_104062721_1:0:0_0:0:0_136/2
+ACAAAAACAAGTCAGATAAGGCAGTCCTCTGGTACATATATAAGAAGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_138405158_138405766_1:1:0_1:0:0_137/2
+CAGGAGGAGCAGGGACGGTCTCTGACGCTGTTGCCTGCCTCTAGATCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_115548969_115549503_0:0:0_1:0:0_138/2
+TACTCTGTTATCTATGCAGACCAGAGCCTAGCATAATTGTTCTCTGAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_195151172_195151687_0:0:0_0:0:1_139/2
+TTTATCAATACACTCAGCTTTCTAGGCAGAGATTTTTAGGATCAAATGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_138103424_138103925_0:0:0_0:0:0_13a/2
+TCTTAAGCAGCATGTTATTAGACAGAAGTAACAATAACATAAAAGTAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_84481564_84482032_1:0:0_0:0:0_13b/2
+CCCCAATCCCCCACCCACCGACTCCCCCTTTTTGGCCCTGGCATTCCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180211651_180212100_2:0:0_1:0:0_13c/2
+AAAAGGACCCAGCCTGCTCCTGCATCCACTGACTTCCTACTTTGCGTTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_19484875_19485375_1:0:0_0:0:0_13d/2
+TGTCTCAGTAACTCCCTCCATGGGTATTTTGTTGACCATTCTAACAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_8815773_8816268_0:0:0_1:0:0_13e/2
+TCAGATATTCTGAGAAGTTTGGGATTTCAGGCATGAAGTCCAGGAAAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_118367902_118368405_1:0:0_0:0:0_13f/2
+GATTTCAGACTGTAAGTCATTTCAATAAAGTGTTTAATATAGAGAGACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_83281820_83282310_2:0:0_3:0:0_140/2
+TGAGGGCTCTAAATCACAAATTCACTAGGATTAGACCAGACTAGTGCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_24810903_24811377_2:0:0_0:0:0_141/2
+AATCGGATAGGGGACTAATATCCAATCTATATAAAGAACTGAAGAATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_24847990_24848482_1:0:0_1:0:0_142/2
+CCCTTTATGTGACTCTATCACATATATCATTCTCATCATCAGCTTGGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_25453923_25454484_1:0:0_2:0:0_143/2
+TTTTTATTTTGTTTTGTTCTTGATTGTTTGATTGTTTGTTTGTTTGAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_35396075_35396608_0:0:0_1:0:0_144/2
+AGGATGACAGTCATACTCAGACCACCATGGCACAAGCCTAGAGACCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_184356181_184356676_1:0:0_1:0:0_145/2
+CCTGGCTGGCCAGTGAGACCCAGGATCAATCCATCTCTGCCTTCCCCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_87890172_87890679_0:0:0_1:0:0_146/2
+TGAGGTGCAAGCATCTGTGTATATGAGTAAAGACCAGAAAGGAGTCTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_192825121_192825655_0:0:0_3:2:0_147/2
+TTTGTTTCTTTCTTTTTTTCTTTCTTTCTTGCTTCCTTCCCTCCTTCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29477154_29477657_0:0:0_0:0:0_148/2
+AATGACAGCATCTTCAATAAATGGTGCTGGCACAACTGGCAGTTATCATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_68360607_68361138_2:1:0_2:0:0_149/2
+GGTCATGTCCTCTTTCTCCGTTGAAGAGGAGGGAATCCGTGTGGGGGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_90679374_90679891_2:0:0_4:0:0_14a/2
+AGTGGGAACATCTGGACCCTTGGCTCCGTAGGCTTATCCCCTTGACAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_90921852_90922384_0:0:0_1:0:0_14b/2
+AGGTAGATCTTGGATCGGGAGTTGGGGAGAGTGAGGTGCACTAGCTGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_144744406_144744790_0:0:0_3:0:0_14c/2
+AGTCTGGCGGTTTCTCAGAAAACTGGACATAGTACTACCGGAGGATCCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157579434_157579959_0:0:0_1:0:0_14d/2
+AGCCAAATGGATGGACCTGGAGGGCATCATCCTGAGTGAGGTAACACAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22354013_22354577_0:0:0_2:0:0_14e/2
+TCTTGAGTTCAAGGCCAGACTGGTCCACAGAACTAGTTATAAGACAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14011029_14011557_0:0:0_1:0:0_14f/2
+CCACCACAAGACTTCGCTACTAAGTCCGAAAATGAGAATGTGCTATTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130418472_130418955_2:0:0_2:0:0_150/2
+GGAGTCTGGTGACTCAATCTCTGGATTTCACACCTGCAATAAACCAGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_150912771_150913298_1:0:0_0:0:0_151/2
+GAGACTATGCTGGGGCCTAGCAAACACAGAAGTGGATGCTCACCGTCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_122600000_122600452_0:0:0_0:0:0_152/2
+AATTTCTAAAATATATAAAATTGTATAATATGATAGAAATGCATATTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_172852130_172852552_1:0:0_2:0:0_153/2
+TAGCTGAGTAGTACTCCATTGTGTAGATGTACGACATTTTCTGTATCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_58219252_58219809_1:0:0_1:0:0_154/2
+CTCTCTTTGCTTTCAAATTTATGGACTCCATTCTTGTTAATTACTGTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_154116562_154116985_0:0:0_0:0:0_155/2
+TTTTTTTAGCTGCTAGGCTTTTGTCTCAGATCAGGATGGTGAGAAAGAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_169424620_169425179_1:0:0_0:0:0_156/2
+TGGCATGAAATGAATGAAAAAAGAAAAAAAGAGAGAGAGAGAAAGAGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72776580_72777093_1:0:0_0:0:0_157/2
+TGAGCAGGCCTAGATTCAGTAAATGGATGGATGACTAAATGGATGGGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_102420738_102421205_2:0:0_1:0:0_158/2
+GGACATTTTCAAAATATCACAGAAGCAAGAAGGACCAAAAGCATAGATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_148315363_148315906_2:0:0_0:0:0_159/2
+AAATGCCATCCTAACAAAAGAAATCTACAGATTCCATTCAATCCTCATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93257911_93258453_0:0:0_1:0:0_15a/2
+CTCAGCTTTCCAATGATTGAAACAAGCTTAGACTCTGACATAGGCCCATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_94169994_94170446_0:0:0_1:0:0_15b/2
+AGGGCAGGAAGAGTGTTCTGTGTGTGGAACCTGGTGGCTGGAGGGCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126263407_126263894_2:0:0_2:0:0_15c/2
+TGTAATGACCGTTATGTGAGCAGCTGGGGAGAAAAGGCAGGTTGTTTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_42763327_42763896_1:0:0_0:0:0_15d/2
+AGCCAGTATCCTTTACCTATAAATACCAAAATAAATAAATAAATAAATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_127932894_127933379_0:0:0_2:0:0_15e/2
+TAAAATACTCACATGCAATGCTGGTGAGGATACCCATCCATCCTATCGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_83608654_83609158_1:0:0_3:0:0_15f/2
+TCCCCTACCCACCCACCACTCCTGTCTTCCCAGCCTGGCATTCTGCTACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_47669914_47670464_0:0:0_0:0:0_160/2
+TGGTGTTAGGCTCTTGTGCATCTTGAGAGAGTTTAAGAAATGGAGTACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133731323_133731869_1:0:0_2:0:0_161/2
+TTTTTTTTTTAACGATTTATTTATTGATTATATGTAAGTACACTGTAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133255321_133255920_0:0:0_1:0:0_162/2
+CTCACTGTCCTCTGTGCTTTAGGATTCTTGCAAGGCCTTTTGAAGTTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_23328420_23328852_0:0:0_1:0:0_163/2
+ACTCAGGACCTCTGGAAGAGCAGTTGGTACTCTTAACAGCTGAGCCATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53072730_53073291_2:0:0_0:0:0_164/2
+CTGCACGCCCATGTTTATTACAGCATTATACCAAGAACAGCAAAGTAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_173130259_173130757_3:0:0_2:0:0_165/2
+CATGCTCTCACTAGTCCAGGCTCTGGCCATATACAGGCTGCCATTTTGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_87397192_87397710_2:0:0_1:0:0_166/2
+AATTTTCTGCTCAATCTAGCAAATAAGACATTTTATCAAGAAACTATATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_187438711_187439219_1:0:0_1:0:0_167/2
+GAAAAGGGGATGGGTGATGGAAAATGGGGAAGAGGCTGTGTGAGGGGGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_123461089_123461580_0:0:0_1:0:0_168/2
+CAAAATGAAATCTCTATCACAGAGACTTGATGCTACAATCCTCCCCAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_181088135_181088642_2:0:0_2:0:0_169/2
+AATCGGGCTTCCAGTTACAAAGTCAGCATGACTCCCTTTTTTGGGAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_167764494_167764902_0:0:0_1:0:0_16a/2
+CCCACCTTCCCCATCTACCCGAGCTCACTATGAGGAGTGCCAGGTTTGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157283727_157284210_1:0:0_0:0:0_16b/2
+ACTTCTTTCTAAATCATTGACAGAACCAGTTCCAAATGTACGATAGGTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_156428357_156428913_4:0:0_3:0:0_16c/2
+TATAGAAAACACTAAACCCCTAACTTTGTCGACAAATAATAAGTAACCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_27945156_27945679_0:0:0_2:0:0_16d/2
+TGGACTCATCTATACTCTCCATTTTCTATTTTTTAAATTATTTTAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_190959090_190959565_0:0:0_0:0:0_16e/2
+CACTTTCTCTTAGTGTCTCCACGGGCTCTGGAGGGACAGGGACAAGTGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163184140_163184589_0:0:0_1:0:0_16f/2
+ACAGAACCGACACACAATTCAAACCAGGTTAATTGGTAAGATGTGGGGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_104189461_104189906_1:0:0_1:0:0_170/2
+CCTGCAAGATTGATTTCTGAAGGGTTGTGTTACTTTTCACATCCACTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_77562742_77563170_2:0:0_0:0:0_171/2
+TACACGTCACTTTTTTAGACAGACATGGGAAATGAACTTCCTTTTTATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192763088_192763581_0:0:0_0:0:0_172/2
+GGGAGCTGCTGAGATCTACGGTTAAAAACATTTTCTATTCATGAAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36839841_36840369_1:0:0_1:0:0_173/2
+GGCAAAGTAGTAGTAAGTAGGGGCACTGTGATACTTGTTTTATCATAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_114603035_114603542_0:0:0_0:0:0_174/2
+ACGTTCATTTTCAATTAACTCTTGTTTACTCATCAAGGTTCTGGTAACCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_57790506_57791066_2:0:0_0:0:0_175/2
+GTTGGTAAAGAAGTTCTGTCAGGACCTGAAACTTTCCTGCTTACTGGGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_35650713_35651282_0:0:0_0:0:0_176/2
+AACTGAGAGATGTATTCATCTGGCTGCTTTCCGCTGAGTCGGGGCAAAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_9711969_9712380_0:0:0_3:0:0_177/2
+ACAGTTGATGCCCTCTTCTGGCCTCTGCAGGCACATATATGATGCACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_89016556_89017046_1:0:0_0:0:0_178/2
+CTGGTGGTTCACTGTCAAGAAACTAGATGGATTGTGACACATGTGATCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132197564_132198148_2:0:0_2:0:0_179/2
+AGTTTGAGAACCACTTGATTAGAAAATGGTGTAACTCCCTGCACCAATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_104335733_104336245_1:0:0_3:0:0_17a/2
+AATACCAAATAGAAAAATGTGAGGCATTATAAAGCCAATTAATGCACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75633066_75633602_2:0:0_1:0:0_17b/2
+GTACCTTTGGATGGTATAGTAATCAGGAGCTCTCCAAAGGACAAGAACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_189869166_189869657_0:0:0_1:0:0_17c/2
+CTACCTGAGTTTGGTCCCCAGGACACGCACAAATAAATGTCATAAATTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_27940779_27941192_2:0:0_0:0:0_17d/2
+TGTCTATGTGCTCTGGTTAGGACTTCACATACTATATGGAATAGATAGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_116796056_116796571_1:0:0_1:0:0_17e/2
+ATATGTACTTCCTGAAGTGGTCCTCTGGCTTCTATTATTTTGCAAAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_20487571_20488054_3:0:0_1:0:0_17f/2
+TGGGGTGCCCATGACTAGGTGGGGTGGGAGTGCTGCGTTCTGATGATGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_70106451_70106893_0:0:0_2:0:0_180/2
+CTTTCTTTTTTTCATTTATTAGATATTTTCTTTATATACATTTCAAATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138350547_138351128_3:0:0_0:0:0_181/2
+GTTTAGTATCACGTGCACACACGGGCCCACCCATAAGTGTAATACATATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103571822_103572343_2:0:0_1:0:0_182/2
+TTCTGCTAAACTACTATCTACAGAAACAATTAAGGAAATGGGCAACTATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_185391115_185391738_5:0:0_0:0:0_183/2
+TGGGTGTCCTGCGTAGCAAACAGGGTGTTGGTGCTTACCGCAGCTTTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_121389447_121389902_0:0:0_0:0:0_184/2
+GCTGCATGTGTGAGGATTTTTTTAAAAAAAGATTTATTTGTATTTGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44088278_44088819_1:0:0_1:0:0_185/2
+TTTTATTTTTCTGAGAGTTTTCACACATGCACTCAGAATGCTCACACAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_57600248_57600747_0:0:0_3:0:0_186/2
+TTAATGGTTTCCTTTGTACAGCATCCATTAGTGCCATTGAGGCTGTTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_105765709_105766274_0:0:0_4:0:0_187/2
+CCATCACCTAGTCCGTATCACAGAGATACAGAGTGAAATACGTTGTCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_158039847_158040318_0:0:0_1:0:0_188/2
+TCACATCTAGATTCAGCTGGCAGTCCAGGCTTCAGCTCCACTCACATTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100649250_100649781_0:0:0_0:0:0_189/2
+TAGAATGGGGATCCTGGAGAGAAGGTTCAGTGGTTGCAAGCACCTTTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_92627120_92627576_1:0:0_1:0:0_18a/2
+TCTAACCCAACTGACTAAAATCCGTGCTGTCCGTACAGATGTGGGTAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_47045474_47045999_2:0:0_2:0:0_18b/2
+CACAACAAGATGCAGTTGTATTGTTATGGTGAGGCCAGCAGAGATGACTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58859721_58860237_3:0:0_1:0:0_18c/2
+TCAGCAAATTGTACGTGCAGAGCGAGGTAACATCAGTTCTGAGGGGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_38899259_38899748_1:0:0_2:0:0_18d/2
+AGCTGCAGAGAACTCACAAGGAATATGCCAATGTGGCCTTGGCTGGATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_43169971_43170448_3:0:0_0:0:0_18e/2
+GAACTCAGGACTGATGGCAAACTAAGGAGCGATGGTAACTTTCTGTCACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_169159076_169159522_0:0:0_2:0:0_18f/2
+GTCTTTGTATGCAGTTAGGCCCCCAACTCATAGAGACCTGCCCCTAGTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14622737_14623201_1:0:0_0:0:0_190/2
+TTGATCAGTAATTGAGAAACTGCCTTACAGTTGGATCTCATGGAGGCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26821729_26822157_1:0:0_3:0:0_191/2
+GATTTTTTAGTAGGGTTTTATTTCAGTGAAGAGGCACGATGACAAGGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_146737011_146737509_0:0:0_0:0:0_192/2
+AGGGAATCTTAGTCTGTGTTGTAGACTACAGACGTATCTGCACTCACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132937628_132938130_1:0:0_0:0:0_193/2
+CAGGAGCTGTATCTCAACCATAACCAGCTCTGCCGCATCTCCCCCAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108674541_108675003_0:0:0_0:0:0_194/2
+GTTTATATAAGGCCTGCCCTTTGCTGGAGCAAAAGAAGGAGGATGAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_155314929_155315340_1:0:0_2:0:0_195/2
+AATAAAATGGCTGTAGGAATTCTGATAGGGATTTCATGAAATGTGTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_76995369_76995845_0:0:0_0:0:0_196/2
+AGGGTTGTTTTGATTTGCATTTCTCTGATGATTAAGGATGCTGAGCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_88758655_88759125_1:0:0_1:0:0_197/2
+GTTGTTGTCCTGGGCGGGTGATGATGTTTAATGCCGGGAGAGGAGGAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_179447008_179447452_1:0:0_1:0:0_198/2
+TGGGATGCGTACCACAGGTCAGAGGACAACTTGTGGAGGCCAGTTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_70539778_70540384_1:0:0_0:0:0_199/2
+TACCAATTCTGAATTATGTAGCTTTTATGTATCTCATTATTATAAATAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_171297998_171298490_3:0:0_2:0:0_19a/2
+ATAACTTTGATCTGAACCAACCACCGGACAGCACTTCCAGCACGTTAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_4703882_4704398_1:0:0_1:0:0_19b/2
+AAATGATGCTTTTGGGTTGTTTTGGACCCTCTCCATAATGTTTAAATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148373552_148374029_0:0:0_2:0:0_19c/2
+ACAGTAGGCTGTGAATATAATTGTTTTTCACCTTCAGGAAAAGGCTAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_165037832_165038374_1:0:0_2:0:0_19d/2
+CACAGGCTGGAGTTATCACAGAGACAGGAGCTTCAGTTGGGGAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117911191_117911633_0:0:0_2:0:0_19e/2
+GCTTCTGGCTATTATAAATAGGGCTGCTATGGATATAGTGGAGCATTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101942751_101943298_2:0:0_2:0:0_19f/2
+GCGAAGGAAATAGATACTAGCCACATTGCCCTGGCGCCATGTAGACAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159291114_159291545_1:0:0_0:0:0_1a0/2
+AACACCCCCACCCCCCCCACCCCCCCGCACGTTTATGGTGCTCGGTTGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26628880_26629394_1:0:0_1:0:0_1a1/2
+TAGGCGTTCCCTCATGCTCCTGGAACTCTGGGTCCTGTTGAAGTTACCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_18997387_18997869_1:0:0_1:0:0_1a2/2
+AAGCAAAATTGGAAAACTAGTTTGGGAATTCCAGAGTAGTATTGGTATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_39575593_39576071_1:0:0_2:0:0_1a3/2
+GGAAGCTAGGATCTCTCAGGAGCCTTGTGGAAAGATGGTGTGTGGACAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_5509844_5510306_2:0:0_1:0:0_1a4/2
+ACACAGCTGGAGTTATGTCAGAGAAAGGAGCTTCATTTGAGGAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_109704460_109704956_1:0:0_0:0:0_1a5/2
+GTATTCAACAAATGAAAGAAATACACTAATAACATTATTTTTACTATGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156587931_156588493_1:0:0_1:0:0_1a6/2
+CGCTGACTCCAGAAGCTACTGGCAGTGGCTGCTGGGAGAGAGAGTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176610586_176611106_1:0:0_0:0:0_1a7/2
+CTTTTGCAATGTGATTAAAAGAAATGCCATCCATTTCCATGTTTTTAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180872448_180872981_1:0:0_3:0:0_1a8/2
+GGCTTCACCAATAGCTTCTCACAGGCTCTCTTCATGGTGTGAAGCCTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_26474215_26474717_2:0:0_1:0:0_1a9/2
+GTCCTCTGATCATTTCTGCACATGGAGCGGTTCTGAGATTGGCGGATGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_104541278_104541749_1:0:0_0:0:0_1aa/2
+GATTTTTATTTTATTTTATTTTATTTTTTGATTGGATATTTTCTTCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67015960_67016373_2:0:0_1:0:0_1ab/2
+ACACCCAGACCAACATTTTTGTCAATAAAATAAAACCCTGTCCTCTATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_29940243_29940732_0:0:0_1:0:0_1ac/2
+GTTTCATTCCAGGGATGCAGGAATTGTTTAATATATGGAAATCCATCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_193079402_193079850_1:0:0_6:0:0_1ad/2
+TCCAGCTCAAAACATCATCAGAAACAGAGTCTACGACTGAAACTGCTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117439972_117440528_1:0:0_0:0:0_1ae/2
+AAAATCTGCCCAACTAGATTAGAGAAATTATCTCAATATTCTAACCTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177239334_177239795_2:0:0_1:0:0_1af/2
+GGGTACTGGTTAGTTCATAATGTTTTTCCACCTATAGGGTTGCAGATCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_158414545_158415096_3:0:0_0:0:0_1b0/2
+TATCTATCACGAGTGTATAATCTCAAGCCCTCGTCCTAATTTTGAAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_97093485_97093964_1:0:0_0:0:0_1b1/2
+GGTCCAACTAAAGAAAGATGTCTCTGATATCACATTCCTGGTGCTTCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67614138_67614777_0:0:0_0:0:0_1b2/2
+TTATTGCTCATCCTGAATATGAGCACACACACACACACACATACACATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_153549562_153550076_0:0:0_1:0:0_1b3/2
+GGCAGGACTGGAGCAGTAGTGTCAGTCTAGAGCGCCAAGTGGCTGCTAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_55425424_55425904_0:1:0_0:0:0_1b4/2
+AAGAATCCAGACAGATGAAAGTTTTTTTTTCTTATTAAAGAATTACCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191019412_191019908_2:0:0_1:0:0_1b5/2
+GTGTGCACACTGCTGAAAAAGGACGCGTTTCTCTTACTGTTTTCGTACCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73180421_73180945_2:0:0_2:0:0_1b6/2
+CTTGAGTTCTTTCTATATATTGGATCTGTTCTTAAGAGCTGTCTCATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_38129466_38129932_2:0:0_2:0:0_1b7/2
+CGGGCGGCAGCTTGGTGATGCGGCGGGTCCCGCGCCACCTCCGCCCAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_133540103_133540570_0:0:0_0:0:0_1b8/2
+CACACACACACACACACACACACACACACGCTTGTGCACATACGTGCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_184916633_184917139_2:0:0_2:0:0_1b9/2
+AAAGAGAAGATCTTGTGGATGGAAATCAAGGCTGCTCTGTCCAGGTAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175669652_175670114_1:0:0_1:0:0_1ba/2
+CAGGGATCCCAAAAGTGTGGTTCCATTTTACAACACAGCTTTGAGTACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_8296849_8297319_1:0:0_0:0:0_1bb/2
+GAATTTGAATAACTACTCATTTACATAAGACATCACAACATTACAGTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_152905590_152906078_1:0:0_1:0:0_1bc/2
+AGTAAACATCAAAGACAAGTCATCAGTGAACAGGCCAACGAGCGGGAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114902352_114902833_0:0:0_0:0:0_1bd/2
+CCATGGAAGGAGTTACAGAGATAAAGTTTGGAGCTGTGATGAAAGGATGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_192964279_192964734_0:0:0_0:0:0_1be/2
+TCTGAAGAGAATGTTCAAAGTTTCATTTCATTTTTATAACTTCTGACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321189_38321768_1:0:0_3:0:0_1bf/2
+TGTCCAAACTGAGCTCAAAAGCCTCCTCTGTAGCTGCTTGAAGGAGATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78900626_78901065_0:0:0_0:0:0_1c0/2
+TCAATTTACTTCTCTTTGACTGCCTTGTGCTTCCAAAGAAACCAGAAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_113540760_113541176_0:0:0_3:0:0_1c1/2
+GTACATACTAAAGTTGAATGTGTCAGGCAAATAAATTGAGAGACTATAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_130677359_130677835_0:0:0_1:0:0_1c2/2
+AACACTGCCTTTTCATTTCTAAGGAGTCTTTTCTTTCTTACTTTTTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180204210_180204758_2:0:0_0:0:0_1c3/2
+TATAGATATTTTAAGCCAACAACAAAGCTATTCTGGCGAGGGATCACATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192984278_192984850_2:0:0_5:0:0_1c4/2
+ATATGGAGTGTGAAAAGATGTCAATGGACATAAAGCAAGTGATCTGAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_176155520_176156071_0:0:0_4:0:0_1c5/2
+GGCCGATTCTCTACTCTAACAGAATGACAGTGTGTCAGAAGGATCCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11299746_11300227_3:0:0_1:0:0_1c6/2
+TACTCATACAACAGATAAAGGCAGTGGAATCCTTAAGACAGGTTTTAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_40475921_40476533_1:0:0_0:0:0_1c7/2
+GCTGGTTTTCTTTCCTTTTCAAAAGATGTTAGGTTTTAAGATTCTGTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_161162459_161162939_0:0:0_0:1:0_1c8/2
+TGTGCATGAGTGTCAACGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56968239_56968712_1:0:0_4:0:0_1c9/2
+TCAACTTGGTGATACAGTCCGACCACCCATTCCCCCATCCCTTATGTCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_90357627_90358090_2:0:0_1:0:0_1ca/2
+ACACATACCATCTACCAAAGACATGTATACACATACACCACACACCACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_184900782_184901265_1:0:0_1:0:0_1cb/2
+GAGCGAGCACTGGCACCTGCGGCTCACCTGGCTGTGTCGGCTCTGCCGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34520052_34520514_0:0:0_0:0:0_1cc/2
+AGAGAGGTGGGAGGGAAATAAGAAGAGAGTGGGGCAGGAGCAGGAGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_121381246_121381739_0:0:0_0:0:0_1cd/2
+TGCTATCCAGATGTAAAGTGAATAAATAAATGAAAAAATTGAAAAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_80355344_80355825_1:0:0_3:0:0_1ce/2
+GCTAACCAAATCCAAGAACACATCAAAAGAATTATCCATCCTGACCAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_23025664_23026100_0:0:0_2:0:0_1cf/2
+GAGTATGGTGCCACTATGTCTTGCTACTATAAATTTCAACTCAAAGCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126877190_126877687_2:0:0_0:0:0_1d0/2
+AGAGTTCAAGCCTTTGTCCATTTCTCAACAGGAAACAGACAGGACCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_64317525_64318044_1:0:0_0:0:0_1d1/2
+GGCCCGCTTTCTATTTATTTGTTTGTTTGTTTATTTATTTATTTATTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_41387597_41388152_2:0:0_4:0:0_1d2/2
+TTCATAATGGAGAATTCAAAGGAACATGAGAGGTAGAAATATTTCTAAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_179273458_179273967_4:0:0_2:0:0_1d3/2
+ACTCTGGAGGCCACACCTTGATGTCTGGTGTTTTCCTCACACTCTCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159718146_159718573_1:0:0_1:0:0_1d4/2
+ACTCTAGTCAATATCATCTATGGAAACTGACTCATTTCCCTTAACCTACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77989741_77990190_3:0:0_2:0:0_1d5/2
+AGGGTATCATCCTGAGTGAGGTAACCCAATCAGAAAGGAACTCGCACCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_70921539_70922106_2:0:0_0:1:0_1d6/2
+GTCAGTATATGATATTTCCTCAGTCTGTCAAATACTCCATGTCAGCGTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_135807545_135808030_2:1:0_0:0:0_1d7/2
+AAGGTAGAGGTGGTGGCTGAGGAGCGCAATGATCTTGAAGCCAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_140999216_140999698_1:0:0_1:0:0_1d8/2
+TCCTCCATGGATGGGCTTGAGAAAGGACCCAAGACTAAACCACCAAAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148512883_148513388_0:0:0_1:0:0_1d9/2
+CTCTCTTTCCACTGATGGCTGACTAGGACATCTTCTGATACATATGCACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_95472009_95472435_1:0:0_0:0:0_1da/2
+GGTTGCCTTTGTCCAGCTTTTATATGAGGGCTGTGTGCCTAGTCCTAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_19217196_19217734_0:0:0_1:0:0_1db/2
+TGTGTGTGTGTTTGTGTGTGTGTGTGTACACGTGTGCACGCGCGTCTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_4075909_4076300_0:0:0_1:0:0_1dc/2
+AAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTTCCTATTCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_186978576_186979074_1:0:0_0:0:0_1dd/2
+CAGAACAAACCAGAGCCCCGTTCATTGTTTTCTGTGGCTTTTGCTATGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_112188833_112189331_0:0:0_1:0:0_1de/2
+TTCAACCTACTACAACTCCCAAATGAATTCCAAAGCATTCCATTGCTTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173609986_173610514_0:0:0_0:0:0_1df/2
+TGCTCAAGAAACAAAGGTGGGACAGTGAAAAAACAACTGGATAAAAGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22017871_22018438_0:0:0_2:0:0_1e0/2
+AGTTCTTAATTTAATAGACTCAGTACATCTTTAGAGTGCCTTGTTTTAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_48541209_48541729_1:0:0_2:0:0_1e1/2
+CGACCCATACAAAGATGTATGAATCTCACTTAGGAAGGTGAATAAAATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_10384181_10384617_2:0:0_0:0:0_1e2/2
+CGAGACATGATAATCAGAACAACAAATGGACTAAATAAAGATAGAATACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_20392227_20392827_2:0:0_0:0:0_1e3/2
+CCCTGACTAAGACACTCTGCTATGCTTGCAGACAGGCGCATGTTGTCCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_171278949_171279483_0:0:0_0:0:0_1e4/2
+TGTTGAGCAAAGAAGCCCCCCTCCTCCCCCCGAAGGCCTATTTTGCTATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58815142_58815652_3:0:0_0:0:0_1e5/2
+GGGGACCCAGTGTGGGTTCCTCAATGGCACCTATCCTCTGAAAAACTAGA
++
+22222222222222222222222222222222222222222222222222
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diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq
new file mode 100644
index 00000000000..6c482fa47c4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out5.fastq
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++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_163976865_163977422_1:0:0_2:0:0_1e9/1
+CCCCCCCCCGACAGATAACATACAGAATAAAAACTTGAACATGCCACACT
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_75768405_75768873_1:0:0_0:0:0_1ea/1
+AAACTGGGCTCAAGGATACCATGCGTTGCTTTATACCAACTTGGACCTGA
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_99777250_99777759_1:0:0_0:0:0_1eb/1
+TCAACTCTAGAGTCCTTCCTAAAAAAAGAAAATGAAAAAAAAAAAAAAAA
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_6944229_6944786_1:0:0_3:0:0_1ec/1
+GATCTAAAATTACCTAGAACATTACATGGAGATGTTGATTAAAGTCATGT
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_6751099_6751639_3:0:0_0:0:0_1ed/1
+ATCCAAATAACTGTTCTCTTTCCATCATATGATACTGACACAGTGATCCC
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_28492407_28492923_0:0:0_2:0:0_1ee/1
+TCTTAGAATGCTATGATTTCACATATCTCTGTATGTTGTAGTAGAAGAGG
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_25977449_25977911_3:0:0_0:0:0_1ef/1
+CAATACAATAATAATGTATCATTATAACAGTAGACAAAAGAAAGGAATAT
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_180012197_180012695_1:0:0_3:0:0_1f0/1
+GAGAACCGTGACTAATATAGAAGTTGGTACCAGGATAGGTTCTAGAGTAA
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_139551031_139551593_1:0:0_0:0:0_1f1/1
+CATCAAGTCAAATTATAGCATTTTTAAAAAGAAACTTGATAGTATATGGC
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_88565594_88566005_0:0:0_1:0:0_1f2/1
+TGTTCAGGCTAGAGTACCTGCATTAGCTCTTCCTTTCTCACACACACTGA
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
+@chr1_28334498_28334996_0:0:0_0:0:0_1f3/1
+AGAGCTCCCTGAGACTAAACCACAATCAAAGAAATCACATGGTGGGACTC
++
+17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out6.fastq b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out6.fastq
new file mode 100644
index 00000000000..094a63da07d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_converter/test-data/fastq_quality_converter-out6.fastq
@@ -0,0 +1,2000 @@
+@chr1_177668195_177668687_1:0:0_2:0:0_0/2
+GGCTGTTCTGTAACTCACTATGTAGACCAGGCTGGTATTCAACTCACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_102240227_102240757_1:0:0_0:0:0_1/2
+ATTGGGAGCCCTATGATCCATCCATTAGCTGACTGTGAGCATCCACTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_135092709_135093083_1:0:0_0:0:0_2/2
+TGTGTACTTGGTAGCAGACAAAGCTGAACTAGACCGTGGCATTAATTCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_173363751_173364238_0:0:0_1:0:0_3/2
+AGTTTCTTTTCCTTGTTATAGCTGTAAGGGATCTGTCTGTTTTTATCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_155990043_155990565_1:0:0_0:0:0_4/2
+CTTTCTATTTTTCTCAAATTAATTACAATCAAAAGTACTTCTGTAACGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_3703883_3704401_0:0:0_1:0:0_5/2
+CCAAGAAGTGGGAGTGGGTGGGTAGAGGAGTGGGAGGGAGGGTATGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148211558_148212105_1:0:0_2:0:0_6/2
+TGCCACACTGTTAAAGACATTTATCTTCCCTCTTGAACACCAATCCCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_30961675_30962138_2:0:0_0:0:0_7/2
+TTTCTGGTCCAGTCTATTTGGTTTTGTGTAGGCTTCTTGTATGATCATGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_86070681_86071151_1:0:0_0:0:0_8/2
+GTTTTATGATATCTTTACATATCCCATCTTTTAAAGTAGCCCTTCTATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_78259267_78259767_0:0:0_1:0:0_9/2
+AACAAAATCTGATGCACTTTTCTGGAGTATCTGAGGACAGCTACAGTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_143451378_143451824_2:0:0_1:0:0_a/2
+TTGATAAAAACTTCATGGTACTGGTATAGAGACATACAAGTAGACCAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163539961_163540475_1:0:0_1:0:0_b/2
+GAGGATGAATGAGTGACTTGAATTGGTGATTTTGAGGTCAAAATGTTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_70390520_70391012_0:0:0_1:0:0_c/2
+AATTTTAAACATCTTATTAACTGAGATCAAAGATATTGATTTTCTATTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_119090463_119090959_0:0:0_0:0:0_d/2
+AAATGTTCACTTTGAAATCACTTCAGACCTACAGGAAAGTTACAAAGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_12587911_12588392_1:0:0_2:0:0_e/2
+ATAATTTCACCTTTTGTCTCTGGGCGCTCATAAAAGATGCTATTGAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_21875665_21876102_0:0:0_1:0:0_f/2
+GGGGCAGAAGACCATGCCACATGAAAGGACCACTTACAGAGCTAGTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_22900274_22900767_0:0:0_0:0:0_10/2
+AATATATTTTAAAAATTCCCCATTGTGGTAGTGTAGACATAGGTCAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_97511239_97511754_1:0:0_0:0:0_11/2
+TGCACTAAATAAAGATAGAATATTAAAAGCAGTAAGGGAAGAAAGGTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_64669865_64670428_2:0:0_2:0:0_12/2
+CTTCTGGTTTTTCTGGCTTTCTACCCCGCAGAAAGTGATTTAGACTACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69102786_69103213_3:0:0_1:0:0_13/2
+ATTTAAATTACACAAAATGAATATTCGAAAAAAGGTACCAAGTTAGTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_117742994_117743506_1:0:0_4:0:0_14/2
+ACAGTCCAGTCTTCACTGACTGCTCCCCATCCCCTACCTCCTCCCCTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_53703453_53703930_0:0:0_1:0:0_15/2
+TTCAACAGAAACCTTTCAGCACGGCTCATGCTTGGGTTGGTTATGTAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17968135_17968661_2:0:0_0:0:0_16/2
+TAAATACAATACATGTTTGATTATGTGTGACTATTATCCATTAAATAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126734590_126735074_2:0:0_1:0:0_17/2
+GGGCAAATGCTTAATTCTTTTGCTCTTCTCGTTTGAAGTTCTTATTGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_15473022_15473574_0:0:0_2:0:0_18/2
+TCCTTCTAATTTCACGTTTTCTTTTTGTTTATAACACAGTGAGTTTCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32809503_32810008_3:0:0_4:0:0_19/2
+CAGGCAAGGCAACTGGAGCTGGAAGTTTAAACCTGCATGTTCATATTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101160086_101160574_0:0:0_2:0:0_1a/2
+AGCATTGGAAATGTAAATGAAGAAAATACCTAATCAAAAAATTTAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86845143_86845638_2:0:0_0:0:0_1b/2
+GGCTTTCCTTGTGGCACTGTCCAATGTCCCTTTAAGGCAAAAGCATGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_156394447_156394901_0:1:0_1:0:0_1c/2
+TTATGGCGAGATGAGCATCTCACTATAGAAATTAAAACTAATCAAAAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175220096_175220545_0:0:0_1:0:0_1d/2
+TCTCATTCAATAGCCTAGACTATTACTTTAAATACAATAAAATTTAATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_66136304_66136892_1:0:0_0:0:0_1e/2
+AAATGGTTTTAGAAGTCCTTATCCTGGGCTTGGATCTTCTCATACCTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_56699450_56700040_1:0:0_0:0:0_1f/2
+TCTTTTAAGTTGACAACTGAGTCTGAGCAGTGATGTTCAATGTATACTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_60449644_60450153_0:0:0_0:0:0_20/2
+GGGAACAGTAGCAGGAACAAGAGGGGTGGGGACAGATGCAGAAGTAGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_28286517_28287074_0:0:0_0:0:0_21/2
+CAATTTTTCTCAGCTTCTGACCAAATTGCTCTGCTTGGCCTCATACTAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_127946423_127946897_1:0:0_1:0:0_22/2
+AATCCTCTTTGTGTAAGAACAGCTGGTGCTGTTAACTTGTCATCTCTCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136274524_136275031_0:0:0_3:0:0_23/2
+GAGGGTGACTTGCTGAAGTCATTTCTCTCCTTTCACCATGTGGGTCCCCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_122372156_122372666_1:0:0_1:0:0_24/2
+GTTTCTGTGTGTCTGTATGTCTGTGAATGTGTGTGTGAGATTTTGTCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_19553027_19553520_1:0:0_0:0:0_25/2
+TTTGCGTATGGTGAAGTATGGGAGCCTTCTTACAACTGAAGAGGTGGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_57071218_57071658_1:0:0_0:0:0_26/2
+CTGTGACTTGGTAAACTCCATGGGGTATCTCCGTACAAGGTGAATGACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_7557012_7557560_0:0:0_2:1:0_27/2
+CAGATTTCCTGACAGTCAAGCTGCCTCTGCATCCCTGAGATCATGCTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18791508_18791966_0:0:0_0:0:0_28/2
+AAGCCAGAGTACGACTGCCCTTACATGAGCCCCATTCCCAATGAGCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_56244256_56244708_0:0:0_0:0:0_29/2
+ATGTTTCCATTTGCATTTAGCTAAAAATTGGCAAGAAGATTGTCATCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_30613322_30613773_2:0:0_1:0:0_2a/2
+GATTGCTTCCAGCTTCTCTCCAATTACTTAGATGTTGGCTACTGGTTTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_161898116_161898586_1:0:0_1:0:0_2b/2
+CACTAATTGAGAAATGCCTTACAGCTGGATCTCATGTAGGCATTTGCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_3742828_3743343_1:0:0_0:0:0_2c/2
+GTCTGGGAAGAACCCAACTGTGTTCTATTTAATCCTGCCCTCCTTCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_59624032_59624611_1:0:0_0:0:0_2d/2
+ATTTATTTATTTATTTATTTATTTATTTATTACACTGTAGCTGTCCTCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_98734890_98735381_1:0:0_2:0:0_2e/2
+AGTAGACACAGTGATTGTACAACAGGACATCTGATGGGACATTAGGACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_170863521_170863976_0:0:0_1:0:0_2f/2
+GTTTTGATTGTAGCCTTCTTCTTCACTTGTAGATGACTGCTTTCTTGCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_111611961_111612483_3:0:0_0:0:0_30/2
+CCCACCTGGGACAGACTAAATGATGCTTAGTTAACTCTAAAATTTCTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_125730124_125730581_1:0:0_1:1:0_31/2
+ATCGTTCCCACATCTTGCTTTCTTATTCCTCACACCCACAACCACAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_10873266_10873801_1:0:0_1:0:0_32/2
+TTCACTGTAGTTGTAACAAATGAGTTGTTTGTTGTGTTTTATAAAAACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175631956_175632547_3:0:0_1:0:0_33/2
+GCCGAGGATGCTATTTAAACATACAAGGTGTCTCATATGAGACTGGGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_20372115_20372592_0:0:0_2:0:0_34/2
+TGTCCTTCTTACCAGAATGGACAGATTGTGGAAACAGAAACATCTATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_172022589_172023145_0:0:0_2:0:0_35/2
+GCCAGGAAAGAGGAGGAAAAAAATAGTCTGACAATACTGCCCCAGCCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_168140019_168140474_0:0:0_1:0:0_36/2
+AGGGATCTGCACAAGTTTGCAGGTGTCTAAGTAGGTCAGAGGTATCAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_12207936_12208461_1:0:0_0:0:0_37/2
+TCATCTCAGACTTGCTATTACAATATCTAATCTTATCTTCTGATAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73438005_73438553_2:0:0_0:0:0_38/2
+TGGCGTGGAGGAAACACTGGTCTCCGTGGACGTCATTTGGCAGTTTTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_152770828_152771350_1:0:0_1:0:0_39/2
+CAGCTACAAGGAGGCACCCGGTCTCTAAAACAGCAAACCAACAAAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_23377131_23377643_1:0:0_1:0:0_3a/2
+ATTTTGTTTTTTTTTTAATCAACGGTAAATACACTGTGCATTATACCCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_101774130_101774651_1:0:0_0:0:0_3b/2
+GATCCAACAAAGATAGAGAACTTCAGACCAATTTCTCTTATGAATATCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_44505664_44506178_2:0:0_1:0:0_3c/2
+GCTGAGGGCCTGATTTTGCCTACTTTTGGACCCATAGGAACAATTTTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136585250_136585783_0:0:0_0:0:0_3d/2
+CTCAGATTGTCAGGTTTGTGGGACAAGTATTTTTTTTACCCACTGAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_125479421_125479942_1:0:0_1:0:0_3e/2
+GACAGGATAGAGGCAGCTAGTAAGCCATGAGGGCAGAGCTTGGGGGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_48288718_48289238_0:0:0_2:0:0_3f/2
+AAAAGATATAGACTAACAGACTGGCTAGACAAACAGGACGCAACATTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_162596088_162596584_0:0:0_1:0:0_40/2
+CAGGACAGCCACGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114964476_114965085_0:0:0_0:0:0_41/2
+ACTCACCATTTTAGTGAGTATACAAGACAAAAACTTGAATAGTCTAATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_132214583_132215104_0:0:0_1:0:0_42/2
+ATGGTGCCAGGGATCCAAACTCATGTTCTTATGTTTGCACAACCTTCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_4422836_4423410_1:0:0_1:0:0_43/2
+TTTTATCACCACAAATATAAGTGGGCCAGTGAGAATGATCAATCCATTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72831428_72831958_1:0:0_0:0:0_44/2
+AACAACAAAAAAAAAAAACCTGGGCTAGCAAGATGGCTCAGTAGGTAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17626572_17627059_2:0:0_0:0:0_45/2
+TTGAGGGAACACACATAGTAACCACCTACAGATAGGATAATTGGAAAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_122621502_122622050_0:0:0_1:0:0_46/2
+TAAACTAATTAATTATAATTTGAGGACAGGAGGGAATTACAGAACATACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_157981625_157982140_2:0:0_1:0:0_47/2
+GACGTCCTACATCCCTTCCAGGCTCAGCTGTTGGTTTTCCCTAGTTACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_86952334_86952916_0:0:0_1:0:0_48/2
+ATTTTGTCCTTCTCAATTTTTTTTCCTTTCTTTGGCTTTAACCTTGCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56589802_56590323_0:0:0_5:0:0_49/2
+CATTACGTGACGGCATTACCCCACAGTACCCACTTTGCTATGCTATTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_44959275_44959852_2:0:0_0:0:0_4a/2
+GGGCACCTGTCCTCCGGTCCAGACGGTGGCTGGCTGTCCCCTGCCCACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78655270_78655764_0:0:0_1:0:0_4b/2
+ATTATAGGTGCTTAGTGGGAAGCTTGATGACCTGAGTTCACCATGGGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_92742731_92743276_3:0:0_1:1:0_4c/2
+TGGGATGCTGAGGTGGGCGGGTATAAGGCAATGGAACTGGTCCATGGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133350357_133350894_2:0:0_0:0:0_4d/2
+GAGAGCGAGAGAAGGTAGAGAAGTAGAAGCCAGTCATTGCCATGCAGAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18383798_18384307_2:0:0_0:0:0_4e/2
+AGGGGGAAAGCCTGTGCTTTTTATTAAAGCATACCTACTGGCTTAGTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_94539200_94539737_1:0:0_1:0:0_4f/2
+AGTTTCAGCGAGAGACAGATAGATGAATGGAATAGAATTGAAGACCCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_131360576_131361118_1:1:0_0:0:0_50/2
+CGTTCCTTCCTACCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_55802170_55802665_0:0:0_1:0:0_51/2
+GAAATACTGCTTTCTCGAGCCTATTAATTATCTTGATATGAACTGAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_160986523_160987031_0:0:0_1:0:0_52/2
+TTGCATTACAAGTGTGAGCCTCTGCATCTGCTTCGCCTACTGTGCGCAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_10207724_10208191_1:0:0_1:0:0_53/2
+CCTGTTAATGGCCACCAGATGGGAGAGGTTCTGAAGAGATTTCCTTCCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_186877031_186877586_1:0:0_0:0:0_54/2
+TCTTGCGCGCGCTCGACTGGGAAGGAAGAACGACGCTGCAACAGGATCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_76761957_76762468_0:0:0_4:0:0_55/2
+TGTTTATAATAGCGAGACGCTTGAAAGAACCCAGCTGCCCCTCAACAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_117599116_117599626_3:0:0_1:0:0_56/2
+TGGCAACAGCAACAGTGAGTGTCTGTGGTGGCTGCATCTGGGATGGACCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_174656805_174657230_0:0:0_2:0:0_57/2
+ACCACACTGTGATTCACAAAGCTAGGAAGCGCTCTCTTAAGTTCTCCCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_31215276_31215715_1:0:0_3:0:0_58/2
+AATGCCTTCCTGGGACTCTGACCAATGGAGCTAATTCCAAAGACCATACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_126165616_126166084_1:0:0_0:0:0_59/2
+AGGATGAAGATTATATGTGAAAGAAGCACTTTGGTAGAGGAAGACTGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_164029809_164030262_1:0:0_2:0:0_5a/2
+TGTTGGGGTGTGGATAAAGTGTATATGAGTTGAAAGGTTGATTTGGTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_121717872_121718374_3:0:0_3:0:0_5b/2
+TATTCTCATGCAATAAACACAAAGCAAATGAAGCCAAAGCTGATGCTCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_160410719_160411215_0:0:0_1:0:0_5c/2
+AGTGTGCTTTTTGTACAAAATCAACAAATGATTTTAATATGATAGTATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100203985_100204499_0:0:0_1:0:0_5d/2
+GAAAGTCTTAGTTCCCATGTCTTACCAGCAGTCTAACTTGCCTTCTTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_177503365_177503816_3:0:0_0:0:0_5e/2
+ACAAGAGGTATGTCTTGGTCTGCCTTACACTGTTTACTTAAGCTGCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_164919242_164919704_1:0:0_1:0:0_5f/2
+CCCAAGCGGAGTAGACGGCAGGAAATAATCAAACTCAGGGGTGAAATCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_36958484_36958940_1:0:0_2:0:0_60/2
+ACCTTAGCCTCCTCCGAGCCGAAAGCCGCAAAGCAACTATTGTCTTTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_99520185_99520697_2:0:0_2:0:0_61/2
+CGACCTGTGATGGTTTGTATATCCTTGGCCCAGGGAGTGGCACCATCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_92584393_92584910_1:0:0_1:0:0_62/2
+AGCTACTGCTCTAACACTATATCTGTCTGCTTCCTGGCATGAAAATCGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_6665937_6666494_1:0:0_2:0:0_63/2
+TAATAATGATGTCAGCATTTCTTTCAGTGCCTCTAGGCCCTCTCTGACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_103781308_103781731_2:0:0_0:0:0_64/2
+ATATGTATCAAAGACAACTCGTCCCAAAAGAACCTTTCTAGTCCTCTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_35981688_35982179_0:0:0_1:0:0_65/2
+CCCTTCCTTGCTTCCTTCTGAAGAACCAGCTTGCCTCCATTTTAGGCTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_76873892_76874342_1:0:0_1:0:0_66/2
+TTCTGTAAGGCTGTGAATCACCCAATTTCTACATGTTTTCAGACCATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_148924276_148924708_1:0:0_0:0:0_67/2
+ACAAACCGTAGATCAACTTTATTACCTCCTTTATTATATTTAGAGGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_48352388_48352886_0:0:0_0:0:0_68/2
+AACATTTTACTATACCATTCAACCATCATTTGAGAAGTTTCCTCCTGCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_135109139_135109668_0:0:0_0:0:0_69/2
+CTGGCCAATGGAGATGCAGCCTATTGTCACAGACATGGTGACAGTGCACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133271389_133271883_0:0:0_0:0:0_6a/2
+CTAACCAAGTTACCCCGAGAAGGGCTGTGCTCTGGAGCGGGGAACTTGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_143528403_143528953_0:0:0_3:0:0_6b/2
+AGTTTTATGAAACTCAGGTCAGCGATCCACACAGCACTTATCACAAGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_60739061_60739616_3:0:0_1:0:0_6c/2
+TTAAGGAATAGTGATTTTTGTTTCCTGTTATTTTTGTTATTAGAGGTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_86239673_86240187_2:0:0_0:0:0_6d/2
+ATGCGTGATTCTAAGGCTGGGCCGCTTGTCCTGAACTGTGTGTGCTGCGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_8425683_8426176_2:0:0_1:0:0_6e/2
+CTTGCTGTGTTTTCGTAGTCTTATACTTTGTGGGAACTAATCCACTGTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34934564_34935093_3:0:0_0:0:0_6f/2
+ATTTATTCATGTATGCTTGAGTATTCATGTAGTAAAGAGAAGACAGCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_43897170_43897709_4:0:0_1:0:0_70/2
+GATAAGGTCACAGTCTGTCAGTGATGCACAGGACAAATCCAAAACCCGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_64512455_64512956_0:0:0_0:0:0_71/2
+AAAGTCAGGAGAGGCTGAAAGCTAGGCCTCTTGTACCAAGCCACTAAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72637152_72637620_2:0:0_2:0:0_72/2
+ATGCCAGTGCACTAACACAAAGCCTGGCATGGTAAGGGACATGCTCGTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_149528405_149528902_2:0:0_0:0:0_73/2
+GTGAAATGATAGACACCAACCCGCTTAAAAAAACTTTCCACCCCAAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_89951120_89951611_2:0:0_1:0:0_74/2
+CCTCGAGGTCGACTCCTCTAGCCCTGCATGGGATATGAGTCGTCCCCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108291981_108292457_1:0:0_1:0:0_75/2
+TTTTGGTTTGTTGAGGGATTACTTTCTTGATTGTTCTAGGGCGTGATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130354891_130355474_0:1:0_0:0:0_76/2
+GATGTGCACAAACATAAAAAACACACACACATGCACACACAAAAAAAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_166207187_166207634_1:0:0_3:1:0_77/2
+CTGAAGTCAGGCCTGGAACTCAAGCAGGACAGGATGCAGGCACAGATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_178111549_178112035_3:0:0_3:0:0_78/2
+TGGACACAAAACATTGAGAATGAGATTGCAACAGGATTCTGTACTACAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_64705135_64705653_1:0:0_3:0:0_79/2
+AATGTACAGTGGGCTTGATATGAAAATATTACAACATATAATTAGATCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_50237028_50237524_0:0:0_2:0:0_7a/2
+TGCAGCTTCTGGGTATTATAAATAAGCCTGCTATGAACATAGTGGAGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_134752385_134752911_2:0:0_0:0:0_7b/2
+CATTCTCTCCTTTGTCTGGCAGTGCCACAGCACAGGGTGCCGTGAGAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_168207741_168208312_2:0:0_0:0:0_7c/2
+GAATGACCCGAGATGTGAGGACTAGGCAGGTTGCTGGGAGGAGGCCATGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_151034392_151034882_0:0:0_0:0:0_7d/2
+ATTAAAGACTTTACAAAAACTAACCTCATGAAACTGAAAAGCTTCTGTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_149618965_149619431_0:0:0_1:0:0_7e/2
+TTAGGTCCCAACACTCACTAAAAAGACAAGGTTTTCCCGCCGTTCTCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_72479618_72480144_1:1:0_0:0:0_7f/2
+GGTGCCAACCACTGTCAAGCTAATAGCAGACTAAAAGTTTTACCGGAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_18771436_18771929_1:0:0_2:0:0_80/2
+TAGTTTTCCAGTGAGGGCTAATAGAACAAAGTGGTATAAATGGTTCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626454_177626877_2:0:0_1:0:0_81/2
+GGTGGTGCAAAGAGAGTCCTGAAGCTGCAGATAGAGTGACAAGAGAAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_58671914_58672334_4:0:0_0:0:0_82/2
+ATTCTTGTGTGACCACGCCCCTAGGATCCTGGGATCCTGGGTGTGTTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_123634655_123635138_1:0:0_1:0:0_83/2
+TCATCCAGAGGTCTGGAATCTTGTTCACAGCACCCATATCTAGCAGCCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_32777949_32778514_0:0:0_2:0:0_84/2
+ATTTCCAAAAATTAAACTTGATCTTCATATTAACTTTCTAATCTACAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321026_38321532_2:0:0_2:0:0_85/2
+TTGCTTACATTCATGGTAGGCCTAACACCACCCAGCATCCTTTGCTTCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_31837668_31838221_1:0:0_2:0:0_86/2
+CCTGGTGTCATTAGCAGAGCCTGGTGGTTTCTGGATTTAACTGGCATTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_189752778_189753180_2:0:0_0:0:0_87/2
+AAGAGAGAGAGAGAGAGATAGCGAGAGAGAGAGAGAGAAAGACAGACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_43602264_43602720_2:0:0_0:0:0_88/2
+TTGTCTTGAGCTGATGATGACATGAGACATTATCCATCTCCAAAATGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_29558267_29558774_2:0:0_0:0:0_89/2
+AATTAGAAAGGGCAATCTGCAAATTCATGTGGAATAACAAAAAACCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_59048796_59049203_1:0:0_0:0:0_8a/2
+TCTGGAACTATAGGACTAAACTTGATTGGCTGATGCTAGGGAGCAGCTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_31285666_31286194_0:0:0_1:0:0_8b/2
+AAACAAAACAAAACAAAACAGATTCAATCATGTTAAGAGGGATAACCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159055630_159056144_1:0:0_3:0:0_8c/2
+GCTCTCTCTAGGAAGGCTCCTTGTTGCCAGACGTCATCCTCTCATTCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163934531_163935036_0:0:0_1:0:0_8d/2
+CAAAGGCTTACCTAAAACAAGCAGTATATGACAGCTAGCTGAAATAAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_116610918_116611481_1:0:0_0:0:0_8e/2
+ACTTAGAATTCTAAATAAAAGGTTAACTGTTTTCTTGGAATGCACTTAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_141208156_141208756_0:0:0_0:0:0_8f/2
+CTGAGTTATGCAGCCTTGCAGAAAGTTCTGGACAGGGTTACTTTTCAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_45492268_45492792_1:0:0_3:0:0_90/2
+AGTACATTAGCAGCCTCTGGAGAAAGAAGATATGCTGCAGTTTGGAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11755179_11755683_0:0:0_1:0:0_91/2
+GGGCTCCCACAAATATTCTAGTATGCTTTGCTCTAGGATAAATAGAATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156738022_156738530_2:0:0_2:0:0_92/2
+GATGCAGTATAAATGGTGTAGCAGATGCCCGAGACCTCAAACACACCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_95480426_95480839_0:0:0_0:0:0_93/2
+TTAAGTGATGTAACTGGATAACAGTAATGAAATTTTAGGTTCTCAGTGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_173460574_173461156_3:0:0_1:0:0_94/2
+TAAATACCAAAAAATGGATTTTGTCAAATAAGGTCTTATAATACCACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_17445381_17445808_2:0:0_4:0:0_95/2
+TAGAAACTGGCAGCCTTTAATTGTCTTGTAGCTTTACCTCTTTGTATGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_76540003_76540477_2:0:0_2:0:0_96/2
+GTGTAGCTCATATGTGACAGCAAACATTGTCCTTGCTGTAACTTTTAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_12896019_12896500_1:0:0_1:0:0_97/2
+ATCCCAGGAGCTTGGTCACACCAGGTTCTCAGGATCACAGAGGCAGCTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_41708628_41709145_0:0:0_1:0:0_98/2
+TACATGTGTGTATATGTGTGCATGGTGTGTACGGTGTGTATGTATGTGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_106826115_106826660_0:0:0_1:0:0_99/2
+TGTCTCATTTATGGGTCTTTAATTCTATTTTATTGATTGACATGTCTGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_13247654_13248181_1:0:0_0:0:0_9a/2
+ATCTGCAGACAGTTCTAACATCTGATGTTCATTTACTACAGACCAGTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117777350_117777861_0:0:0_1:0:0_9b/2
+AAATGTACTCACTGATAAGTGGATATTAACCCAGAAACTTAGTATAGCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77191506_77192008_2:0:0_1:0:0_9c/2
+TAAAAAAAAAAACTCTTTAGTTTGGCTTGCATGTGATTCAAGGTTTCCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36849743_36850269_1:0:0_1:0:0_9d/2
+TCTTTCTAGAACAGACTCCAGTTCAATAACCATTTATTGGTTGGGTGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_148890840_148891366_0:0:0_0:0:0_9e/2
+AATCTAAAATTTGAACCCCTTATACCCTTCAAATCCACCATCAACTGTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_84671373_84671880_2:0:0_1:0:0_9f/2
+TTCTAGGGACATTCTTTTCTTTCTACAGATTTCGATAATTAAAGGAGAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102434771_102435253_0:0:0_1:0:0_a0/2
+ACTTCCTCTTGGTTAGTTGTCCAGTGAGTTCTACATTGGTCTGTCTCTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_100209819_100210321_0:0:0_1:0:0_a1/2
+TCTAAATGGGATGTGGCTAAGCTGGCAGTTTGCTGGCTTAGCATTTATGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_62044005_62044573_2:0:0_1:0:0_a2/2
+GTCAGACATCAGCATCACAAATGCAGAATGACAGAAATTGACTTGCACCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_85132332_85132871_1:0:0_3:0:0_a3/2
+CAAAAGAAAACATTTAATTGGGGCTTTTTTACAGTTTCAAAAAATAGGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58843215_58843696_0:0:0_0:0:0_a4/2
+CGTGCCAGAAGAAGAGAGTGACTCCTCTGGAACTGGAGATACAGGCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_137975188_137975732_1:0:0_1:1:0_a5/2
+TGGCCAGATACAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_141967561_141968074_0:0:0_0:0:0_a6/2
+TCAACATATATGACATCCATAAATCAATGATTTGACTATGAAACCATGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8624607_8625140_1:0:0_1:0:0_a7/2
+TTAACTTTCAAGACAAGTGAATACTATATGATTTGGTGATTCTATGCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_138783244_138783650_1:0:0_1:0:0_a8/2
+GATACTCATGTGTGTGCCCAGCGGCTCTTTGAAGCTTACGTTCTTACATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_52699200_52699639_1:0:0_1:0:0_a9/2
+TCGCCACCGTCTGCTGTCACCTGAATTTTTGATCTTAGCCCTTCTGACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_32849205_32849709_0:0:0_0:0:0_aa/2
+AAGTCAGAGGAAGCAGCCAGAATTAGCTGGAGCACCATGAGAAGCACCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_182043596_182044137_0:0:0_0:0:0_ab/2
+AAAGAAAAGAAAAGAAAAGAAAAGAAAAAATGGACAAGAAGGCAAATAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_136004325_136004842_4:0:0_0:0:0_ac/2
+AATCAGCTAGTTGGTTTGTCAGAGGAACTCTCAAGAGAAGATAGCACTAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_174545541_174546018_2:0:0_1:0:0_ad/2
+TGTCTGAGGCATTCTGCAGAGCTGCGTTACTTTGTTTTGTTGAAAGGTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11117502_11117925_0:0:0_1:0:0_ae/2
+CACTGCATATACTATTGACCTAGTCTGACATAATACCTCACTTTCCTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_44177515_44177974_0:0:0_3:0:0_af/2
+CTCAAGAAGAACTAAACCCACACAGAAGTACCTTGGTCAATATTTCACAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72645507_72646002_0:0:0_0:0:0_b0/2
+AGCCCCAATGAAATATTTCATGATGTTTCTTTACAGGAATAGAAACCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_147283777_147284272_0:0:0_1:0:0_b1/2
+TGCTCCCTTTTATTTTTGTTGTTAGAGTTGGGATTCTGTTCTTGTGGCTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_133675964_133676447_1:0:0_0:0:0_b2/2
+CATGTCAATGTGTGGGTCTGTTTGTAGGTATGTGCCTGAGCGAGCAAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_114568587_114569130_0:0:0_0:0:0_b3/2
+TCCGAGTTGGGGTTTACTATTCTTATTTGTTTAGTAAGATATTAAAGGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_111695385_111695895_0:0:0_0:0:0_b4/2
+TGATTTTCTCATCCGTAGATGAGTGGGCTTTTAACCTTGGCTTGGGTGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_172273320_172273788_1:0:0_0:0:0_b5/2
+AAGAAAACACTATTCCATAGGAACCTGAAGCCAGCTTCCCGTCTCAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29014340_29014871_0:0:0_2:0:0_b6/2
+GCAAGGCTCCATCTCCTACTAGCACCACTCCCTATGGGCCAAGTATTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177626521_177627066_1:1:0_0:0:0_b7/2
+GACCGGCACCTCTCACTGTGACCATTTTGAGTTTCTTGCTCTAAACTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_110742845_110743354_1:0:0_0:0:0_b8/2
+CATCCAATAGATGACTGAGCATCCACTTCTGTATTTGCCAGGTACTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14101155_14101687_3:0:0_0:0:0_b9/2
+CTAAGGTAAATTAGATCTTCCACCTTTGATTTACCCAGTTCTCCCAAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_38147934_38148475_0:0:0_0:0:0_ba/2
+TCCATCTGGAGTATTCAGAGGGCCCTTGAGGTTTGATGCTCATCCACGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_84834550_84834957_2:0:0_1:0:0_bb/2
+AGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGCTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_94046734_94047311_0:2:0_1:0:0_bc/2
+CTGTGGAACAGGAAGTCGAAAATTCTAATCAGGATTCTCTTGGTTAAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138724568_138725155_1:0:0_2:0:0_bd/2
+GATCTTCCCTTGGCTCAGCATTATTAAGGAAGGTGCTGGCTGAACCAGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_105672406_105672966_0:0:0_1:0:0_be/2
+TCAATTACTACCATTTTGTGCATATTTTAAAAGCACACTATGGACACACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_157814995_157815529_0:0:0_3:0:0_bf/2
+TGACATACAAGTAATAAAGCCAAATACTTAAATAGGCCATCTCTGTTACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130059190_130059641_1:0:0_0:0:0_c0/2
+GTTGGGGGTTGGGGAAATCTTTAGGAAGTTCCAGAGACCTGAGACAGGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18604367_18604942_1:0:0_0:0:0_c1/2
+TAGCGGTACACTGTGTGAGCTCTAGGAAAATACAGAGCTCAGGAGATTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_160029930_160030407_0:0:0_1:0:0_c2/2
+CAGATAGCTAGCTTATGGACTAAGATTTTTTTTTAGAGTGGCTTAGTACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_32417120_32417575_0:0:0_3:0:0_c3/2
+AGTTATACATGTTGTGGTGGACCCCAGCAACAAAATTACTTCCATTCCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_91572336_91572825_0:0:0_3:0:0_c4/2
+CACCTTCAGGAACTGTTAGAGGTGGTTCCTGTTGCTCTTACGCCCCCCGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_167308006_167308522_0:0:0_0:0:0_c5/2
+GCCCGATCGCCTACCTCACACTAGAACCCTGTCACACGGTGGCTGGACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53658226_53658697_1:0:0_1:0:0_c6/2
+GTTCTTTTGTAATTGCGTTACCTCACTCAGGATAATGCCCTCCATGTCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75542501_75543075_2:0:0_0:0:0_c7/2
+AAGTTCTCTCTCGCCAAGGTAGAAGCTAGAAAAATGCATATGTCCTGACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_49392954_49393517_0:0:0_2:0:0_c8/2
+GTATCTTTTTCTCTCCTTTTCATTTTTTAAAGTTTATTGTTGTTCTTAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_18890524_18891056_1:0:0_0:0:0_c9/2
+AGTTGATTCCGGACTCTTCAGAGTCCAGCTTTTTGGGGGTTTTGTTTTTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_13661516_13661931_1:0:0_1:0:0_ca/2
+AAAAGGAGTAGGCTAAGGTAGTGAATACACTCTACATCTCTATTGTGGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69507936_69508419_2:0:0_1:0:0_cb/2
+CACCTCGAGAAAGAGCCAACCATAGAGCATGTGTGTTGATTGTTTAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_171186227_171186672_2:0:0_1:0:0_cc/2
+CCCTTCTCTCTTCTAGAAACCAGACAATCCGTCCTTATACTCTCTAGTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_151167139_151167658_0:0:0_3:0:0_cd/2
+TCCAAATTAGACAGACTTCCTCTTCCTGTGGCCTGGACTGTTTTTTCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_166490443_166490901_1:0:0_2:0:0_ce/2
+GATGTCAGAAACATGATAGGTCTCAGAATGTGAGGATTTTAATCCCAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78053476_78053981_1:0:0_0:0:0_cf/2
+ATAGCATATCCCCTTAGCCAGAGAGCTTAGACTGGAGAAGCACAGCTGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_27573317_27573793_0:0:0_2:0:0_d0/2
+TTTAAGCTTATATAATAAAAAACATAATTACAAATCTATACAAAAGTATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_74520986_74521432_1:0:0_4:0:0_d1/2
+TTTCCTTATAAAGTCTGAGAGTTTAGTTAGTGCTGACTTGTCAGAAACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_194568812_194569255_1:0:0_0:0:0_d2/2
+AAGTACCATCTGTATTAATGATTCACAGTTATTTAAATATTTGAACAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173094678_173095086_1:0:0_0:0:0_d3/2
+TAAGGTTGAGTTTCTGATAGGATACCATGAGGTAAAGATTTCCAAGCAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_125473775_125474200_1:0:0_0:0:0_d4/2
+GCAGCTTGACTCCGGTTGTGATTAATCAAAAGAGGTGACCCTGGGAGACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_60312834_60313394_2:0:0_1:0:0_d5/2
+GAAGGAACGGGAAGGAGAAATGGTGTAATTAAATTATAATCTCAAAAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_21769340_21769783_1:0:0_1:0:0_d6/2
+GGCTAAGATCAAAACTTCAGGTGACCGCAGATGCTGGCGAGGATGTGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_29011734_29012196_0:0:0_0:0:0_d7/2
+AATCAGATTTTGTGTTTTGTTTGGTTTTCCATTAATGCTTTCACAACGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_55988735_55989188_1:0:0_0:0:0_d8/2
+AAGATTAGTTCTAAAGACATTACAGCTGCCACTCCAAGTTCTTGCCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_143689772_143690244_0:0:0_2:0:0_d9/2
+TCTAGTTAATTAACACTGTTATTACTTTACATGTTGCTCCATTTTGTGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102292799_102293241_0:0:0_2:0:0_da/2
+GAATACGATTACTAATTCGTTGAGAAGGTGATATGGCCATTCACAAAACG
++
+22222222222222222222222222222222222222222222222222
+@chr1_175815890_175816392_0:0:0_1:0:0_db/2
+AACATTTCAACCTCTCCATGGCACTGAAGTTTTAATCAGCCAATCAGGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_65030887_65031423_1:0:0_0:0:0_dc/2
+TAATGTTATTCCTGAGATTTTTCCAGAGAAACAAATCCCACCATTTTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_77446136_77446727_1:0:0_0:0:0_dd/2
+GGACTACTTTCACTAAAGTGGAAAAACTCAATGGTGCTGTGAAACCTCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_79825884_79826306_1:0:0_0:0:0_de/2
+CAGGGGAACACCAGGGCCAAAAAGGGGGAGTGGGTGGGCAGGGGAGTGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_142137580_142138145_0:0:0_1:0:0_df/2
+GCCTCTAACAGTACCAAGGCTAAGCTGTTCACTATGACTTCATACCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77524851_77525306_1:0:0_2:0:0_e0/2
+GCAAGCTCCCGAAATCACAAGTTTGCAGACCAGGCAATGGGAAATTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26694201_26694676_0:0:0_0:0:0_e1/2
+ACAATCGAATCATTATCTAGATATTTTGATTATCTTTGCTTTAGGTTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_93157579_93158060_0:0:0_1:0:0_e2/2
+CCTTTGGGATTCTCCATCCAATGAGCCTCAGTTTCCTTACGAGAGGGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_93554302_93554745_0:0:0_1:0:0_e3/2
+ACAGGATGCAGCTGGAGACTTCAACACCTTACCTCCAATAATAGTCATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_115859373_115859816_1:0:0_1:0:0_e4/2
+GCATGCATCAAAGCAATGGTCCCTTAAAGCAGAGGAGTCAAGACTTTTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_59908209_59908731_3:0:0_0:0:0_e5/2
+CTTGTTGTCTAAAAGGACTGAAAGGCAAGATTGGCTGCTGAGGTACTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_154628329_154628794_2:0:0_1:0:0_e6/2
+TGTACAGACACTTTATAGGTGTCTTTGGTGACTTTGGTGACACTCTGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38934187_38934653_1:0:0_1:0:1_e7/2
+TTATAGCTTGCAATAGAAAATGGAGTTTTGTTTTTGCCAAATAAATGGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176440703_176441215_3:0:0_1:0:0_e8/2
+GGACCGAGCCAGTCTAGATATTGCAGAACTAAGAGTGTGTCTGTGAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_146248574_146249007_1:0:0_0:0:0_e9/2
+GAATAGATTGTACAGAATCAATAACCTACCAAGCATTTGCCTAGGGACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_137417062_137417534_1:0:0_0:0:0_ea/2
+ATGCCCAGTCACCCACAGTTGGTCTCCTGTCTCAGCCCCAATAACTAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_55607180_55607772_1:0:0_0:0:0_eb/2
+GGCACATCATTATCCATTGGTAAGCTTTGCTTTTTCCACAAGGTCACTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_174928179_174928755_0:0:0_1:0:0_ec/2
+AATTGCAAATAATTTTTATCCCATTTTGTATGTATGATAACTGATACCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_113923154_113923648_3:0:0_1:0:0_ed/2
+TAATGTGAGGTTACCTCTGGCACTGAGGACTATTAAGTGGCTTTAAATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_78423064_78423594_1:0:0_0:0:0_ee/2
+AACTTGATATATGTTACTGTGGACCAAATGCCCTTCCTTCTCCAGTATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_154582561_154583019_0:0:0_1:0:0_ef/2
+CAGCAGCCTTGTTTGTAGTCTTATTATGAATTCAACAATATGTCACATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_181723357_181723842_1:0:0_2:0:0_f0/2
+CATGGCCATTTTCAAGACTCAGGTTGTGGACATCACACTAAGTGAGATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176206787_176207249_1:0:0_1:0:0_f1/2
+TGTGACAGTCTCTGGTGGCCTTACACTCCTCCTCTTTTTGCCTCTATGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156026308_156026788_0:1:0_2:0:0_f2/2
+ATTTTATTTTCAAAGCACTAAATTATTAGAATATTTTACCTTTTTATATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_55128175_55128671_1:0:0_0:0:0_f3/2
+CAGAGCAGTGAGCGAGTTTCCTGGAGAGGCCCGTGAGGGGACAGTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_184447109_184447646_1:0:0_1:1:0_f4/2
+GTTATATAACCTCATAGCAGTCACCAAATGAAATAAGACATTCCTCGTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_194617734_194618226_0:0:0_0:0:0_f5/2
+GTGATTCTCACATTTATTCTTCCTCTATTATTGTTTATGTCTGCATGTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_80810218_80810755_0:0:0_0:0:0_f6/2
+AGAGAAAGGCAGAGAAATAGAAGAGAGAGAGAGACCTACCTCTGATAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_144296368_144296930_2:0:0_2:0:0_f7/2
+ATAGTTCCTTTTGACATAGATCCTTCTAAAGGAATTGTAAGGGAATGTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108312503_108312946_1:0:0_2:0:0_f8/2
+GTTAAACAAGCATGCAATCCCACCAACAATGTAGGAGTGTTCCCCTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_78228179_78228640_0:1:0_0:0:0_f9/2
+CTGAGTCTTGTTTGAGGATGGATGAACTGATATAAACGTTTTCAAAAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_52088998_52089426_1:0:0_1:0:0_fa/2
+CTGTCCTGTCTTCCCTCTCCTCCGATCCCTCTTCTGAGTACTGAGCTTAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_30782403_30782942_1:0:0_0:0:0_fb/2
+AATATATTCACCTACACCTGTTAACTCAAAGGATCTGCTTCAATACTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_6435675_6436268_3:0:0_2:0:0_fc/2
+GACTCATTCATTCCCAGAGAGGAACAAAGGAAAATACCACAGGCATTTCG
++
+22222222222222222222222222222222222222222222222222
+@chr1_164237997_164238538_0:0:0_0:0:0_fd/2
+CATCAGACAGACTTCCAGATAAAACGGGTTTCAGATGAGATCAGTACTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_187097969_187098475_2:0:0_2:0:0_fe/2
+CCATAGCAGCTGTGTGGAAGTCATGACTCCTGGAGGTCAAGTGACTATAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44694856_44695375_3:0:0_1:1:0_ff/2
+TTCCATAATATCTCTTACTATCAATGGACTCAATTCGCCAATAAAAAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_111782668_111783223_1:0:0_3:0:0_100/2
+GCTCTATCCCGTGGATGGCTGTGAGCATCCCCTTCTATTTGTCAGGCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_94206847_94207360_1:0:0_1:0:0_101/2
+AAGCAAAACTGAGAAGCGGCAAGGAGGAGAGAACAGAATGGAACATCACG
++
+22222222222222222222222222222222222222222222222222
+@chr1_132119789_132120286_3:0:0_1:0:0_102/2
+GGCAGGTAGGCGGCGGGCGGACAGGCCGGGCAGCTCAGTGAACTCATATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_34226734_34227203_0:0:0_0:0:0_103/2
+AGCGGGCTACTGATAGCCCACAGGTTCAAACCAGACAAAATCACAGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_138105716_138106319_4:0:0_1:0:0_104/2
+ATAAACAATCATGGCTCCTTAATTAACACAAATACTTTGAGGTCTCAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_126030856_126031342_1:0:0_2:0:0_105/2
+CAATTGTTGTAGAAACATTTCAAGAAAAGCGTGTATACAATTCACTAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_118807485_118808058_0:0:0_1:0:0_106/2
+TTCCGAAAAAGAAATAAGCAGAAAGCTGTTTGACTTTTCCTGGGGTGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_19849114_19849606_2:0:0_0:0:0_107/2
+TTCCTTAGGGTGCTGTGGTGAAGGTCTTTTATGACAGCAAATGGCAAATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_66877733_66878136_2:0:0_1:0:0_108/2
+GAGCATCATAATGGCCCATCGGTATCAAAGCTAAGACACGAGCATGGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132522495_132522987_0:0:0_1:0:0_109/2
+GCCCTGACTAGTGTAATAGGCCACAAGACGAAATGGAGCCTAGATTCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117050436_117050942_0:0:0_1:0:0_10a/2
+ACCCAATCACAAAAGAATACACATGATGCGCCCTCACTGATAATCGGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_125967212_125967705_0:0:0_0:0:0_10b/2
+TCAGGGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_69313718_69314189_1:0:0_2:0:0_10c/2
+TTTTCGTAGATGACACTATCACCTCTGCGTATCTGACCTCATCCTCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_60897368_60897871_1:0:0_1:0:0_10d/2
+TTCTCTAGCTTCTCCATTGGGGGCCCTGTGTTCCATCCTATAGATGGCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_174325015_174325549_0:1:0_2:0:0_10e/2
+TTAGAAATAACTTCAGAATGTCTTTTTGCCCCGTACAAATAAATAAGCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_85055965_85056468_2:0:0_0:0:0_10f/2
+CATAGAGAACATCGGCACAACAATCAAAGAAAATGGAAAATGCAAAAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_131415777_131416249_5:0:0_1:0:0_110/2
+TTTTGATCTCCTAACCAAAGGAAGATCTCCCAGTTTCATTGGTTCCAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67136277_67136702_3:0:0_0:0:0_111/2
+GTGCCATTCTGCTTTACTCAAGTGTTCTCCGTTTTACAATTCAGGAAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8402131_8402528_1:0:0_2:0:0_112/2
+TAGTTCTTATTACCATTTGGTTGATTTCACCCCTGATTTTGATTATTTCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_155126875_155127345_1:0:0_3:0:0_113/2
+TTGGCCAGCGTGAGATACATGCGACCCTGTTTAAAAAAAAAAAATCAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_93916438_93916928_0:0:0_0:0:0_114/2
+GGCAGTGATGTCTGAGGAGGACTCTTTGGGCAGATCTGAGGCCTGCTCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_135734641_135735118_0:0:0_0:0:0_115/2
+GTTGGGCAACCAGTTCATAGCACCACAGCTGTAGGAGGCAGAACTGGATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44391025_44391499_0:0:0_1:0:0_116/2
+TTAGCCAAATTAGAGGGTCGTCTTGAGGCACCTCAGAGACCAGAGTCTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_110722550_110723095_2:0:0_4:0:0_117/2
+ATATAGTAAAATATATCATTGTTTGTATCTAAGCCATTATATAGATACGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_185586471_185586808_1:0:0_0:0:0_118/2
+GCTTTCTGGTCTGATTTGACTCTTAGCGAAGGTAAATGTTCACGCACCGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_182936908_182937483_1:0:0_2:0:0_119/2
+CAAGCAGACACATTCATGAGGATTCTATCTGATTCTTCAACTTTTATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_136882207_136882635_0:0:0_2:0:0_11a/2
+GTTTGGTATTTGAAAATAATGTCTGTGTAATGGATTATGAGAACGGACTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22027558_22028086_0:0:0_2:0:0_11b/2
+CCCTGGAAGCTCTGTGGAGTCTGGTTGGTTGATATTGTTGTTTTTCCTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101069088_101069523_0:0:0_0:0:0_11c/2
+CTCCAGCTTGTTTCTTCAGACCTTTTGCTTGGAAAATTGTTTTCCAGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133430180_133430643_0:0:0_3:0:0_11d/2
+CCTGAGATCCTGTCACTTGATCTGAAGTTTTGCCTTCTGTCTCCCCTGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_141505317_141505766_0:0:0_2:0:0_11e/2
+TTATATGCCCCAGTACAGGGGAACACCAGGGTCAAAAATTGGGAATGGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103387516_103388014_1:0:0_1:0:0_11f/2
+ATGATTTCCCTACCTGATGAAGGCTTACTTCTTTCTTCACCTTATTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_134753416_134753860_0:0:0_1:0:0_120/2
+GGACCTGGGCTTAGGGGACAGCAGCAGTCTGACCTCGGCAACAGGGAGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_168048225_168048764_3:0:0_0:0:0_121/2
+CTATCATGATCACATTACCCTTACATCACCATCATCACGAGCCCATCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_15110325_15110842_0:0:0_1:0:0_122/2
+TATGGTTGTATTAAAGTTGACTAATATTAAGAGCTTAAATAGATTTAAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_71511848_71512298_1:0:0_1:0:0_123/2
+GCTTATTAATCCTCTTCTCTTCTTGTATAAAGGGTGGGAAGTAGGTGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_37275066_37275622_2:0:0_0:0:0_124/2
+GCTGGTTTCCAAATCACAGAGACCTCTCCTGCCTCTACTTCCTGAATCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191970326_191970894_1:0:0_0:0:0_125/2
+TCGTTAAGAGTAACCAGGGCTCTTAACTGCTGAGCCATCTCTTAGACTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_137258018_137258449_1:0:0_1:0:0_126/2
+TATTGTGAAGTGTTATGTCTGATTGGCTTTTTCTCTTCTTCGGTGAGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_163885263_163885763_1:0:0_0:0:0_127/2
+TGCAAACCCTTTCAGCTCCTTGGGTACATTCTCTAGCTCCTTCATTGGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_95122061_95122611_1:0:0_2:0:0_128/2
+ATCATCATAGGTGGGCAAAGGAAAGTGTGAAATAGTATAATTTCATGGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191245641_191246131_1:0:0_1:0:0_129/2
+TTCTTGAGAGAGGCCAGGCTTTGGGGAACAGATGTCGCACAGCACTAAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_11721955_11722368_1:0:0_3:0:0_12a/2
+GGGTTGGAGATCCCTTTAGCTCCTTGGGTGGTTTCCCTAGCACCTCCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_102954712_102955237_1:0:0_1:0:0_12b/2
+AAGTGGTGTAACCCAATCACAAAAGTACATACAGGATATACACTCACTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_26914346_26914925_0:0:0_1:0:0_12c/2
+AAGGGGAAAAAAAACCCTGCATCTGATATGCAAAGACCAGTCAGAATAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_151053369_151053909_1:0:0_0:0:0_12d/2
+TCTTCTGTCTTGAAAAAGAAAAAGAACACACCACACCCACACACCACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93621447_93621970_1:1:0_1:0:0_12e/2
+CATTAAGTGTTAGTTTTAATAGCGCATTGAAAACCCTACCATTTCAATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_13530953_13531445_0:0:0_0:0:0_12f/2
+GAGTTCATTAGTACATTGGTTGTTTGGAACACAGAAAATCTTTCCCCATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_154530120_154530631_2:0:0_4:0:0_130/2
+AGGCTTTACTTAATCCAAAGCATAAGTACATTGTTTGACACCCTGCAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_100109085_100109588_0:0:0_2:0:0_131/2
+TCACAGAGGACACTCACAGAGATGAACCATGCTCCCAGGGACAAGATGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_150348101_150348543_0:0:0_0:0:0_132/2
+ATTAAACCTGCTGAGTTATTTGAATTCCAGAGACTTACATAATAAACTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_8725925_8726392_0:0:0_3:1:0_133/2
+TATTCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_189147844_189148204_2:0:0_1:0:0_134/2
+TTAAGACATATTAATTTTAGGAAGTAAAAATAAATTCATTTAAATTGGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_45618673_45619149_2:0:0_2:0:0_135/2
+CTGGATGTCGCTTGTGCAGATCTTGAAAATTTTGTCATAATTGCTGGGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_104062147_104062721_1:0:0_0:0:0_136/2
+ACAAAAACAAGTCAGATAAGGCAGTCCTCTGGTACATATATAAGAAGAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_138405158_138405766_1:1:0_1:0:0_137/2
+CAGGAGGAGCAGGGACGGTCTCTGACGCTGTTGCCTGCCTCTAGATCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_115548969_115549503_0:0:0_1:0:0_138/2
+TACTCTGTTATCTATGCAGACCAGAGCCTAGCATAATTGTTCTCTGAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_195151172_195151687_0:0:0_0:0:1_139/2
+TTTATCAATACACTCAGCTTTCTAGGCAGAGATTTTTAGGATCAAATGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_138103424_138103925_0:0:0_0:0:0_13a/2
+TCTTAAGCAGCATGTTATTAGACAGAAGTAACAATAACATAAAAGTAACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_84481564_84482032_1:0:0_0:0:0_13b/2
+CCCCAATCCCCCACCCACCGACTCCCCCTTTTTGGCCCTGGCATTCCCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180211651_180212100_2:0:0_1:0:0_13c/2
+AAAAGGACCCAGCCTGCTCCTGCATCCACTGACTTCCTACTTTGCGTTGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_19484875_19485375_1:0:0_0:0:0_13d/2
+TGTCTCAGTAACTCCCTCCATGGGTATTTTGTTGACCATTCTAACAAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_8815773_8816268_0:0:0_1:0:0_13e/2
+TCAGATATTCTGAGAAGTTTGGGATTTCAGGCATGAAGTCCAGGAAAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_118367902_118368405_1:0:0_0:0:0_13f/2
+GATTTCAGACTGTAAGTCATTTCAATAAAGTGTTTAATATAGAGAGACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_83281820_83282310_2:0:0_3:0:0_140/2
+TGAGGGCTCTAAATCACAAATTCACTAGGATTAGACCAGACTAGTGCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_24810903_24811377_2:0:0_0:0:0_141/2
+AATCGGATAGGGGACTAATATCCAATCTATATAAAGAACTGAAGAATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_24847990_24848482_1:0:0_1:0:0_142/2
+CCCTTTATGTGACTCTATCACATATATCATTCTCATCATCAGCTTGGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_25453923_25454484_1:0:0_2:0:0_143/2
+TTTTTATTTTGTTTTGTTCTTGATTGTTTGATTGTTTGTTTGTTTGAGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_35396075_35396608_0:0:0_1:0:0_144/2
+AGGATGACAGTCATACTCAGACCACCATGGCACAAGCCTAGAGACCAGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_184356181_184356676_1:0:0_1:0:0_145/2
+CCTGGCTGGCCAGTGAGACCCAGGATCAATCCATCTCTGCCTTCCCCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_87890172_87890679_0:0:0_1:0:0_146/2
+TGAGGTGCAAGCATCTGTGTATATGAGTAAAGACCAGAAAGGAGTCTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_192825121_192825655_0:0:0_3:2:0_147/2
+TTTGTTTCTTTCTTTTTTTCTTTCTTTCTTGCTTCCTTCCCTCCTTCCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_29477154_29477657_0:0:0_0:0:0_148/2
+AATGACAGCATCTTCAATAAATGGTGCTGGCACAACTGGCAGTTATCATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_68360607_68361138_2:1:0_2:0:0_149/2
+GGTCATGTCCTCTTTCTCCGTTGAAGAGGAGGGAATCCGTGTGGGGGAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_90679374_90679891_2:0:0_4:0:0_14a/2
+AGTGGGAACATCTGGACCCTTGGCTCCGTAGGCTTATCCCCTTGACAGGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_90921852_90922384_0:0:0_1:0:0_14b/2
+AGGTAGATCTTGGATCGGGAGTTGGGGAGAGTGAGGTGCACTAGCTGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_144744406_144744790_0:0:0_3:0:0_14c/2
+AGTCTGGCGGTTTCTCAGAAAACTGGACATAGTACTACCGGAGGATCCAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157579434_157579959_0:0:0_1:0:0_14d/2
+AGCCAAATGGATGGACCTGGAGGGCATCATCCTGAGTGAGGTAACACAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22354013_22354577_0:0:0_2:0:0_14e/2
+TCTTGAGTTCAAGGCCAGACTGGTCCACAGAACTAGTTATAAGACAGCCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14011029_14011557_0:0:0_1:0:0_14f/2
+CCACCACAAGACTTCGCTACTAAGTCCGAAAATGAGAATGTGCTATTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130418472_130418955_2:0:0_2:0:0_150/2
+GGAGTCTGGTGACTCAATCTCTGGATTTCACACCTGCAATAAACCAGCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_150912771_150913298_1:0:0_0:0:0_151/2
+GAGACTATGCTGGGGCCTAGCAAACACAGAAGTGGATGCTCACCGTCAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_122600000_122600452_0:0:0_0:0:0_152/2
+AATTTCTAAAATATATAAAATTGTATAATATGATAGAAATGCATATTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_172852130_172852552_1:0:0_2:0:0_153/2
+TAGCTGAGTAGTACTCCATTGTGTAGATGTACGACATTTTCTGTATCCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_58219252_58219809_1:0:0_1:0:0_154/2
+CTCTCTTTGCTTTCAAATTTATGGACTCCATTCTTGTTAATTACTGTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_154116562_154116985_0:0:0_0:0:0_155/2
+TTTTTTTAGCTGCTAGGCTTTTGTCTCAGATCAGGATGGTGAGAAAGAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_169424620_169425179_1:0:0_0:0:0_156/2
+TGGCATGAAATGAATGAAAAAAGAAAAAAAGAGAGAGAGAGAAAGAGAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_72776580_72777093_1:0:0_0:0:0_157/2
+TGAGCAGGCCTAGATTCAGTAAATGGATGGATGACTAAATGGATGGGTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_102420738_102421205_2:0:0_1:0:0_158/2
+GGACATTTTCAAAATATCACAGAAGCAAGAAGGACCAAAAGCATAGATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_148315363_148315906_2:0:0_0:0:0_159/2
+AAATGCCATCCTAACAAAAGAAATCTACAGATTCCATTCAATCCTCATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_93257911_93258453_0:0:0_1:0:0_15a/2
+CTCAGCTTTCCAATGATTGAAACAAGCTTAGACTCTGACATAGGCCCATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_94169994_94170446_0:0:0_1:0:0_15b/2
+AGGGCAGGAAGAGTGTTCTGTGTGTGGAACCTGGTGGCTGGAGGGCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126263407_126263894_2:0:0_2:0:0_15c/2
+TGTAATGACCGTTATGTGAGCAGCTGGGGAGAAAAGGCAGGTTGTTTGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_42763327_42763896_1:0:0_0:0:0_15d/2
+AGCCAGTATCCTTTACCTATAAATACCAAAATAAATAAATAAATAAATAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_127932894_127933379_0:0:0_2:0:0_15e/2
+TAAAATACTCACATGCAATGCTGGTGAGGATACCCATCCATCCTATCGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_83608654_83609158_1:0:0_3:0:0_15f/2
+TCCCCTACCCACCCACCACTCCTGTCTTCCCAGCCTGGCATTCTGCTACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_47669914_47670464_0:0:0_0:0:0_160/2
+TGGTGTTAGGCTCTTGTGCATCTTGAGAGAGTTTAAGAAATGGAGTACCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_133731323_133731869_1:0:0_2:0:0_161/2
+TTTTTTTTTTAACGATTTATTTATTGATTATATGTAAGTACACTGTAGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_133255321_133255920_0:0:0_1:0:0_162/2
+CTCACTGTCCTCTGTGCTTTAGGATTCTTGCAAGGCCTTTTGAAGTTCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_23328420_23328852_0:0:0_1:0:0_163/2
+ACTCAGGACCTCTGGAAGAGCAGTTGGTACTCTTAACAGCTGAGCCATCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_53072730_53073291_2:0:0_0:0:0_164/2
+CTGCACGCCCATGTTTATTACAGCATTATACCAAGAACAGCAAAGTAATG
++
+22222222222222222222222222222222222222222222222222
+@chr1_173130259_173130757_3:0:0_2:0:0_165/2
+CATGCTCTCACTAGTCCAGGCTCTGGCCATATACAGGCTGCCATTTTGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_87397192_87397710_2:0:0_1:0:0_166/2
+AATTTTCTGCTCAATCTAGCAAATAAGACATTTTATCAAGAAACTATATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_187438711_187439219_1:0:0_1:0:0_167/2
+GAAAAGGGGATGGGTGATGGAAAATGGGGAAGAGGCTGTGTGAGGGGGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_123461089_123461580_0:0:0_1:0:0_168/2
+CAAAATGAAATCTCTATCACAGAGACTTGATGCTACAATCCTCCCCAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_181088135_181088642_2:0:0_2:0:0_169/2
+AATCGGGCTTCCAGTTACAAAGTCAGCATGACTCCCTTTTTTGGGAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_167764494_167764902_0:0:0_1:0:0_16a/2
+CCCACCTTCCCCATCTACCCGAGCTCACTATGAGGAGTGCCAGGTTTGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_157283727_157284210_1:0:0_0:0:0_16b/2
+ACTTCTTTCTAAATCATTGACAGAACCAGTTCCAAATGTACGATAGGTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_156428357_156428913_4:0:0_3:0:0_16c/2
+TATAGAAAACACTAAACCCCTAACTTTGTCGACAAATAATAAGTAACCTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_27945156_27945679_0:0:0_2:0:0_16d/2
+TGGACTCATCTATACTCTCCATTTTCTATTTTTTAAATTATTTTAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_190959090_190959565_0:0:0_0:0:0_16e/2
+CACTTTCTCTTAGTGTCTCCACGGGCTCTGGAGGGACAGGGACAAGTGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_163184140_163184589_0:0:0_1:0:0_16f/2
+ACAGAACCGACACACAATTCAAACCAGGTTAATTGGTAAGATGTGGGGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_104189461_104189906_1:0:0_1:0:0_170/2
+CCTGCAAGATTGATTTCTGAAGGGTTGTGTTACTTTTCACATCCACTAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_77562742_77563170_2:0:0_0:0:0_171/2
+TACACGTCACTTTTTTAGACAGACATGGGAAATGAACTTCCTTTTTATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192763088_192763581_0:0:0_0:0:0_172/2
+GGGAGCTGCTGAGATCTACGGTTAAAAACATTTTCTATTCATGAAATTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_36839841_36840369_1:0:0_1:0:0_173/2
+GGCAAAGTAGTAGTAAGTAGGGGCACTGTGATACTTGTTTTATCATAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_114603035_114603542_0:0:0_0:0:0_174/2
+ACGTTCATTTTCAATTAACTCTTGTTTACTCATCAAGGTTCTGGTAACCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_57790506_57791066_2:0:0_0:0:0_175/2
+GTTGGTAAAGAAGTTCTGTCAGGACCTGAAACTTTCCTGCTTACTGGGAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_35650713_35651282_0:0:0_0:0:0_176/2
+AACTGAGAGATGTATTCATCTGGCTGCTTTCCGCTGAGTCGGGGCAAAGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_9711969_9712380_0:0:0_3:0:0_177/2
+ACAGTTGATGCCCTCTTCTGGCCTCTGCAGGCACATATATGATGCACAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_89016556_89017046_1:0:0_0:0:0_178/2
+CTGGTGGTTCACTGTCAAGAAACTAGATGGATTGTGACACATGTGATCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132197564_132198148_2:0:0_2:0:0_179/2
+AGTTTGAGAACCACTTGATTAGAAAATGGTGTAACTCCCTGCACCAATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_104335733_104336245_1:0:0_3:0:0_17a/2
+AATACCAAATAGAAAAATGTGAGGCATTATAAAGCCAATTAATGCACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75633066_75633602_2:0:0_1:0:0_17b/2
+GTACCTTTGGATGGTATAGTAATCAGGAGCTCTCCAAAGGACAAGAACTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_189869166_189869657_0:0:0_1:0:0_17c/2
+CTACCTGAGTTTGGTCCCCAGGACACGCACAAATAAATGTCATAAATTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_27940779_27941192_2:0:0_0:0:0_17d/2
+TGTCTATGTGCTCTGGTTAGGACTTCACATACTATATGGAATAGATAGGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_116796056_116796571_1:0:0_1:0:0_17e/2
+ATATGTACTTCCTGAAGTGGTCCTCTGGCTTCTATTATTTTGCAAAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_20487571_20488054_3:0:0_1:0:0_17f/2
+TGGGGTGCCCATGACTAGGTGGGGTGGGAGTGCTGCGTTCTGATGATGGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_70106451_70106893_0:0:0_2:0:0_180/2
+CTTTCTTTTTTTCATTTATTAGATATTTTCTTTATATACATTTCAAATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_138350547_138351128_3:0:0_0:0:0_181/2
+GTTTAGTATCACGTGCACACACGGGCCCACCCATAAGTGTAATACATATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_103571822_103572343_2:0:0_1:0:0_182/2
+TTCTGCTAAACTACTATCTACAGAAACAATTAAGGAAATGGGCAACTATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_185391115_185391738_5:0:0_0:0:0_183/2
+TGGGTGTCCTGCGTAGCAAACAGGGTGTTGGTGCTTACCGCAGCTTTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_121389447_121389902_0:0:0_0:0:0_184/2
+GCTGCATGTGTGAGGATTTTTTTAAAAAAAGATTTATTTGTATTTGTATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_44088278_44088819_1:0:0_1:0:0_185/2
+TTTTATTTTTCTGAGAGTTTTCACACATGCACTCAGAATGCTCACACAAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_57600248_57600747_0:0:0_3:0:0_186/2
+TTAATGGTTTCCTTTGTACAGCATCCATTAGTGCCATTGAGGCTGTTCTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_105765709_105766274_0:0:0_4:0:0_187/2
+CCATCACCTAGTCCGTATCACAGAGATACAGAGTGAAATACGTTGTCTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_158039847_158040318_0:0:0_1:0:0_188/2
+TCACATCTAGATTCAGCTGGCAGTCCAGGCTTCAGCTCCACTCACATTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_100649250_100649781_0:0:0_0:0:0_189/2
+TAGAATGGGGATCCTGGAGAGAAGGTTCAGTGGTTGCAAGCACCTTTTTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_92627120_92627576_1:0:0_1:0:0_18a/2
+TCTAACCCAACTGACTAAAATCCGTGCTGTCCGTACAGATGTGGGTAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_47045474_47045999_2:0:0_2:0:0_18b/2
+CACAACAAGATGCAGTTGTATTGTTATGGTGAGGCCAGCAGAGATGACTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58859721_58860237_3:0:0_1:0:0_18c/2
+TCAGCAAATTGTACGTGCAGAGCGAGGTAACATCAGTTCTGAGGGGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_38899259_38899748_1:0:0_2:0:0_18d/2
+AGCTGCAGAGAACTCACAAGGAATATGCCAATGTGGCCTTGGCTGGATCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_43169971_43170448_3:0:0_0:0:0_18e/2
+GAACTCAGGACTGATGGCAAACTAAGGAGCGATGGTAACTTTCTGTCACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_169159076_169159522_0:0:0_2:0:0_18f/2
+GTCTTTGTATGCAGTTAGGCCCCCAACTCATAGAGACCTGCCCCTAGTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_14622737_14623201_1:0:0_0:0:0_190/2
+TTGATCAGTAATTGAGAAACTGCCTTACAGTTGGATCTCATGGAGGCATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26821729_26822157_1:0:0_3:0:0_191/2
+GATTTTTTAGTAGGGTTTTATTTCAGTGAAGAGGCACGATGACAAGGGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_146737011_146737509_0:0:0_0:0:0_192/2
+AGGGAATCTTAGTCTGTGTTGTAGACTACAGACGTATCTGCACTCACACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_132937628_132938130_1:0:0_0:0:0_193/2
+CAGGAGCTGTATCTCAACCATAACCAGCTCTGCCGCATCTCCCCCAGGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_108674541_108675003_0:0:0_0:0:0_194/2
+GTTTATATAAGGCCTGCCCTTTGCTGGAGCAAAAGAAGGAGGATGAATGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_155314929_155315340_1:0:0_2:0:0_195/2
+AATAAAATGGCTGTAGGAATTCTGATAGGGATTTCATGAAATGTGTAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_76995369_76995845_0:0:0_0:0:0_196/2
+AGGGTTGTTTTGATTTGCATTTCTCTGATGATTAAGGATGCTGAGCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_88758655_88759125_1:0:0_1:0:0_197/2
+GTTGTTGTCCTGGGCGGGTGATGATGTTTAATGCCGGGAGAGGAGGAGTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_179447008_179447452_1:0:0_1:0:0_198/2
+TGGGATGCGTACCACAGGTCAGAGGACAACTTGTGGAGGCCAGTTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_70539778_70540384_1:0:0_0:0:0_199/2
+TACCAATTCTGAATTATGTAGCTTTTATGTATCTCATTATTATAAATAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_171297998_171298490_3:0:0_2:0:0_19a/2
+ATAACTTTGATCTGAACCAACCACCGGACAGCACTTCCAGCACGTTAGTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_4703882_4704398_1:0:0_1:0:0_19b/2
+AAATGATGCTTTTGGGTTGTTTTGGACCCTCTCCATAATGTTTAAATGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148373552_148374029_0:0:0_2:0:0_19c/2
+ACAGTAGGCTGTGAATATAATTGTTTTTCACCTTCAGGAAAAGGCTAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_165037832_165038374_1:0:0_2:0:0_19d/2
+CACAGGCTGGAGTTATCACAGAGACAGGAGCTTCAGTTGGGGAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117911191_117911633_0:0:0_2:0:0_19e/2
+GCTTCTGGCTATTATAAATAGGGCTGCTATGGATATAGTGGAGCATTTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_101942751_101943298_2:0:0_2:0:0_19f/2
+GCGAAGGAAATAGATACTAGCCACATTGCCCTGGCGCCATGTAGACAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159291114_159291545_1:0:0_0:0:0_1a0/2
+AACACCCCCACCCCCCCCACCCCCCCGCACGTTTATGGTGCTCGGTTGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_26628880_26629394_1:0:0_1:0:0_1a1/2
+TAGGCGTTCCCTCATGCTCCTGGAACTCTGGGTCCTGTTGAAGTTACCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_18997387_18997869_1:0:0_1:0:0_1a2/2
+AAGCAAAATTGGAAAACTAGTTTGGGAATTCCAGAGTAGTATTGGTATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_39575593_39576071_1:0:0_2:0:0_1a3/2
+GGAAGCTAGGATCTCTCAGGAGCCTTGTGGAAAGATGGTGTGTGGACAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_5509844_5510306_2:0:0_1:0:0_1a4/2
+ACACAGCTGGAGTTATGTCAGAGAAAGGAGCTTCATTTGAGGAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_109704460_109704956_1:0:0_0:0:0_1a5/2
+GTATTCAACAAATGAAAGAAATACACTAATAACATTATTTTTACTATGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_156587931_156588493_1:0:0_1:0:0_1a6/2
+CGCTGACTCCAGAAGCTACTGGCAGTGGCTGCTGGGAGAGAGAGTCACTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_176610586_176611106_1:0:0_0:0:0_1a7/2
+CTTTTGCAATGTGATTAAAAGAAATGCCATCCATTTCCATGTTTTTAAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180872448_180872981_1:0:0_3:0:0_1a8/2
+GGCTTCACCAATAGCTTCTCACAGGCTCTCTTCATGGTGTGAAGCCTCAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_26474215_26474717_2:0:0_1:0:0_1a9/2
+GTCCTCTGATCATTTCTGCACATGGAGCGGTTCTGAGATTGGCGGATGGC
++
+22222222222222222222222222222222222222222222222222
+@chr1_104541278_104541749_1:0:0_0:0:0_1aa/2
+GATTTTTATTTTATTTTATTTTATTTTTTGATTGGATATTTTCTTCATTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67015960_67016373_2:0:0_1:0:0_1ab/2
+ACACCCAGACCAACATTTTTGTCAATAAAATAAAACCCTGTCCTCTATTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_29940243_29940732_0:0:0_1:0:0_1ac/2
+GTTTCATTCCAGGGATGCAGGAATTGTTTAATATATGGAAATCCATCAAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_193079402_193079850_1:0:0_6:0:0_1ad/2
+TCCAGCTCAAAACATCATCAGAAACAGAGTCTACGACTGAAACTGCTTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_117439972_117440528_1:0:0_0:0:0_1ae/2
+AAAATCTGCCCAACTAGATTAGAGAAATTATCTCAATATTCTAACCTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_177239334_177239795_2:0:0_1:0:0_1af/2
+GGGTACTGGTTAGTTCATAATGTTTTTCCACCTATAGGGTTGCAGATCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_158414545_158415096_3:0:0_0:0:0_1b0/2
+TATCTATCACGAGTGTATAATCTCAAGCCCTCGTCCTAATTTTGAAACAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_97093485_97093964_1:0:0_0:0:0_1b1/2
+GGTCCAACTAAAGAAAGATGTCTCTGATATCACATTCCTGGTGCTTCAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_67614138_67614777_0:0:0_0:0:0_1b2/2
+TTATTGCTCATCCTGAATATGAGCACACACACACACACACATACACATAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_153549562_153550076_0:0:0_1:0:0_1b3/2
+GGCAGGACTGGAGCAGTAGTGTCAGTCTAGAGCGCCAAGTGGCTGCTAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_55425424_55425904_0:1:0_0:0:0_1b4/2
+AAGAATCCAGACAGATGAAAGTTTTTTTTTCTTATTAAAGAATTACCTGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_191019412_191019908_2:0:0_1:0:0_1b5/2
+GTGTGCACACTGCTGAAAAAGGACGCGTTTCTCTTACTGTTTTCGTACCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_73180421_73180945_2:0:0_2:0:0_1b6/2
+CTTGAGTTCTTTCTATATATTGGATCTGTTCTTAAGAGCTGTCTCATTTC
++
+22222222222222222222222222222222222222222222222222
+@chr1_38129466_38129932_2:0:0_2:0:0_1b7/2
+CGGGCGGCAGCTTGGTGATGCGGCGGGTCCCGCGCCACCTCCGCCCAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_133540103_133540570_0:0:0_0:0:0_1b8/2
+CACACACACACACACACACACACACACACGCTTGTGCACATACGTGCTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_184916633_184917139_2:0:0_2:0:0_1b9/2
+AAAGAGAAGATCTTGTGGATGGAAATCAAGGCTGCTCTGTCCAGGTAACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_175669652_175670114_1:0:0_1:0:0_1ba/2
+CAGGGATCCCAAAAGTGTGGTTCCATTTTACAACACAGCTTTGAGTACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_8296849_8297319_1:0:0_0:0:0_1bb/2
+GAATTTGAATAACTACTCATTTACATAAGACATCACAACATTACAGTAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_152905590_152906078_1:0:0_1:0:0_1bc/2
+AGTAAACATCAAAGACAAGTCATCAGTGAACAGGCCAACGAGCGGGAGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_114902352_114902833_0:0:0_0:0:0_1bd/2
+CCATGGAAGGAGTTACAGAGATAAAGTTTGGAGCTGTGATGAAAGGATGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_192964279_192964734_0:0:0_0:0:0_1be/2
+TCTGAAGAGAATGTTCAAAGTTTCATTTCATTTTTATAACTTCTGACATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_38321189_38321768_1:0:0_3:0:0_1bf/2
+TGTCCAAACTGAGCTCAAAAGCCTCCTCTGTAGCTGCTTGAAGGAGATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_78900626_78901065_0:0:0_0:0:0_1c0/2
+TCAATTTACTTCTCTTTGACTGCCTTGTGCTTCCAAAGAAACCAGAAAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_113540760_113541176_0:0:0_3:0:0_1c1/2
+GTACATACTAAAGTTGAATGTGTCAGGCAAATAAATTGAGAGACTATAAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_130677359_130677835_0:0:0_1:0:0_1c2/2
+AACACTGCCTTTTCATTTCTAAGGAGTCTTTTCTTTCTTACTTTTTTTCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_180204210_180204758_2:0:0_0:0:0_1c3/2
+TATAGATATTTTAAGCCAACAACAAAGCTATTCTGGCGAGGGATCACATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_192984278_192984850_2:0:0_5:0:0_1c4/2
+ATATGGAGTGTGAAAAGATGTCAATGGACATAAAGCAAGTGATCTGAGTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_176155520_176156071_0:0:0_4:0:0_1c5/2
+GGCCGATTCTCTACTCTAACAGAATGACAGTGTGTCAGAAGGATCCAAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_11299746_11300227_3:0:0_1:0:0_1c6/2
+TACTCATACAACAGATAAAGGCAGTGGAATCCTTAAGACAGGTTTTAACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_40475921_40476533_1:0:0_0:0:0_1c7/2
+GCTGGTTTTCTTTCCTTTTCAAAAGATGTTAGGTTTTAAGATTCTGTGTG
++
+22222222222222222222222222222222222222222222222222
+@chr1_161162459_161162939_0:0:0_0:1:0_1c8/2
+TGTGCATGAGTGTCAACGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_56968239_56968712_1:0:0_4:0:0_1c9/2
+TCAACTTGGTGATACAGTCCGACCACCCATTCCCCCATCCCTTATGTCCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_90357627_90358090_2:0:0_1:0:0_1ca/2
+ACACATACCATCTACCAAAGACATGTATACACATACACCACACACCACAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_184900782_184901265_1:0:0_1:0:0_1cb/2
+GAGCGAGCACTGGCACCTGCGGCTCACCTGGCTGTGTCGGCTCTGCCGCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_34520052_34520514_0:0:0_0:0:0_1cc/2
+AGAGAGGTGGGAGGGAAATAAGAAGAGAGTGGGGCAGGAGCAGGAGCAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_121381246_121381739_0:0:0_0:0:0_1cd/2
+TGCTATCCAGATGTAAAGTGAATAAATAAATGAAAAAATTGAAAAAAAAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_80355344_80355825_1:0:0_3:0:0_1ce/2
+GCTAACCAAATCCAAGAACACATCAAAAGAATTATCCATCCTGACCAAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_23025664_23026100_0:0:0_2:0:0_1cf/2
+GAGTATGGTGCCACTATGTCTTGCTACTATAAATTTCAACTCAAAGCAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_126877190_126877687_2:0:0_0:0:0_1d0/2
+AGAGTTCAAGCCTTTGTCCATTTCTCAACAGGAAACAGACAGGACCTTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_64317525_64318044_1:0:0_0:0:0_1d1/2
+GGCCCGCTTTCTATTTATTTGTTTGTTTGTTTATTTATTTATTTATTTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_41387597_41388152_2:0:0_4:0:0_1d2/2
+TTCATAATGGAGAATTCAAAGGAACATGAGAGGTAGAAATATTTCTAAGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_179273458_179273967_4:0:0_2:0:0_1d3/2
+ACTCTGGAGGCCACACCTTGATGTCTGGTGTTTTCCTCACACTCTCCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_159718146_159718573_1:0:0_1:0:0_1d4/2
+ACTCTAGTCAATATCATCTATGGAAACTGACTCATTTCCCTTAACCTACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_77989741_77990190_3:0:0_2:0:0_1d5/2
+AGGGTATCATCCTGAGTGAGGTAACCCAATCAGAAAGGAACTCGCACCAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_70921539_70922106_2:0:0_0:1:0_1d6/2
+GTCAGTATATGATATTTCCTCAGTCTGTCAAATACTCCATGTCAGCGTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_135807545_135808030_2:1:0_0:0:0_1d7/2
+AAGGTAGAGGTGGTGGCTGAGGAGCGCAATGATCTTGAAGCCAAATGCCT
++
+22222222222222222222222222222222222222222222222222
+@chr1_140999216_140999698_1:0:0_1:0:0_1d8/2
+TCCTCCATGGATGGGCTTGAGAAAGGACCCAAGACTAAACCACCAAAGAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_148512883_148513388_0:0:0_1:0:0_1d9/2
+CTCTCTTTCCACTGATGGCTGACTAGGACATCTTCTGATACATATGCACC
++
+22222222222222222222222222222222222222222222222222
+@chr1_95472009_95472435_1:0:0_0:0:0_1da/2
+GGTTGCCTTTGTCCAGCTTTTATATGAGGGCTGTGTGCCTAGTCCTAATT
++
+22222222222222222222222222222222222222222222222222
+@chr1_19217196_19217734_0:0:0_1:0:0_1db/2
+TGTGTGTGTGTTTGTGTGTGTGTGTGTACACGTGTGCACGCGCGTCTTGG
++
+22222222222222222222222222222222222222222222222222
+@chr1_4075909_4076300_0:0:0_1:0:0_1dc/2
+AAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTTCCTATTCTCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_186978576_186979074_1:0:0_0:0:0_1dd/2
+CAGAACAAACCAGAGCCCCGTTCATTGTTTTCTGTGGCTTTTGCTATGAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_112188833_112189331_0:0:0_1:0:0_1de/2
+TTCAACCTACTACAACTCCCAAATGAATTCCAAAGCATTCCATTGCTTAA
++
+22222222222222222222222222222222222222222222222222
+@chr1_173609986_173610514_0:0:0_0:0:0_1df/2
+TGCTCAAGAAACAAAGGTGGGACAGTGAAAAAACAACTGGATAAAAGCTT
++
+22222222222222222222222222222222222222222222222222
+@chr1_22017871_22018438_0:0:0_2:0:0_1e0/2
+AGTTCTTAATTTAATAGACTCAGTACATCTTTAGAGTGCCTTGTTTTAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_48541209_48541729_1:0:0_2:0:0_1e1/2
+CGACCCATACAAAGATGTATGAATCTCACTTAGGAAGGTGAATAAAATAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_10384181_10384617_2:0:0_0:0:0_1e2/2
+CGAGACATGATAATCAGAACAACAAATGGACTAAATAAAGATAGAATACT
++
+22222222222222222222222222222222222222222222222222
+@chr1_20392227_20392827_2:0:0_0:0:0_1e3/2
+CCCTGACTAAGACACTCTGCTATGCTTGCAGACAGGCGCATGTTGTCCAC
++
+22222222222222222222222222222222222222222222222222
+@chr1_171278949_171279483_0:0:0_0:0:0_1e4/2
+TGTTGAGCAAAGAAGCCCCCCTCCTCCCCCCGAAGGCCTATTTTGCTATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_58815142_58815652_3:0:0_0:0:0_1e5/2
+GGGGACCCAGTGTGGGTTCCTCAATGGCACCTATCCTCTGAAAAACTAGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_157206264_157206747_1:0:0_3:0:0_1e6/2
+AAAGATTAAATTGTATGTACATTATTCTCTTTCATTCTCTCTTAGATATC
++
+22222222222222222222222222222222222222222222222222
+@chr1_130727486_130727887_0:0:0_1:0:0_1e7/2
+TCCAGATAACCCAACAGAAAAGGGATTTATCCCAGTTATTGATGAAGATA
++
+22222222222222222222222222222222222222222222222222
+@chr1_56227774_56228368_1:0:0_2:0:0_1e8/2
+GGTCTTTCATTGGGCTTCTTCCACTAAAGGAAACATGAGAAGAGTGGACA
++
+22222222222222222222222222222222222222222222222222
+@chr1_163976865_163977422_1:0:0_2:0:0_1e9/2
+GGAGTGTTTTTATTGACAGGTGTTAGTGCTTTTATAAAAAAAAACTATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_75768405_75768873_1:0:0_0:0:0_1ea/2
+TGTTGTGAAACCTGAAGATGGAGAGAGACAGAGATAGATAAAAGAGACAG
++
+22222222222222222222222222222222222222222222222222
+@chr1_99777250_99777759_1:0:0_0:0:0_1eb/2
+GTACTGTAGACCAAATTAATAAACAACACATACAAATAAATCCAAGAGAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_6944229_6944786_1:0:0_3:0:0_1ec/2
+ACCTGATCTACCATGGAGCTCCAAGTAGGAAGGACAGAACTGATTGGTAT
++
+22222222222222222222222222222222222222222222222222
+@chr1_6751099_6751639_3:0:0_0:0:0_1ed/2
+GAGACTGGGATGTAAAGTGAATAAGTAAACAGAGTATTTCTTGTTTATTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_28492407_28492923_0:0:0_2:0:0_1ee/2
+CCGCATAGTGCCAGTAACAGATGCAAGCTTACAACTTGATCCCCACCTGA
++
+22222222222222222222222222222222222222222222222222
+@chr1_25977449_25977911_3:0:0_0:0:0_1ef/2
+TTTCCCCCCATTCAAGTCTTTTAGTTTGTTCTTGTGAGGCACTGAGTTTA
++
+22222222222222222222222222222222222222222222222222
+@chr1_180012197_180012695_1:0:0_3:0:0_1f0/2
+TGTGTGGAATACGATGACGATAGATGAGGCATTCTGTTTGATTTTCTGCA
++
+22222222222222222222222222222222222222222222222222
+@chr1_139551031_139551593_1:0:0_0:0:0_1f1/2
+ACTAATAGACAACCATTTACTCTGATTCAACTGGCTGCCAATTTCTGAGT
++
+22222222222222222222222222222222222222222222222222
+@chr1_88565594_88566005_0:0:0_1:0:0_1f2/2
+ACAGACAACATGGAGAACATGGGGAGGGGGCAATGAAAAGTATTAAAGCC
++
+22222222222222222222222222222222222222222222222222
+@chr1_28334498_28334996_0:0:0_0:0:0_1f3/2
+GAGGACTCCAAAGGATGTCAAAGACTTCACAGTAAGTACTCTGGGCAGGA
++
+22222222222222222222222222222222222222222222222222
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml
new file mode 100644
index 00000000000..ee402e15395
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/.shed.yml
@@ -0,0 +1,10 @@
+categories:
+- Fastq Manipulation
+description: Filter by quality
+long_description: |
+  This tool filters reads based on quality scores.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fastq_quality_filter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml
new file mode 100644
index 00000000000..2101eeb6948
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml
@@ -0,0 +1,82 @@
+<tool id="cshl_fastq_quality_filter" version="1.0.1" name="Filter by quality">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastq_quality_filter
+-q $quality
+-p $percent
+-v
+-o '$output'
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastq_input" />
+
+        <param name="quality" type="integer" value="20" label="Quality cut-off value"/>
+
+        <param name="percent" type="integer" value="90"
+            label="Percent of bases in sequence that must have quality equal to / higher than cut-off value" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Test1:  100% of bases with quality 33 or higher (pretty steep requirement...) -->
+            <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
+            <param name="quality" value="33"/>
+            <param name="percent" value="100"/>
+            <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" />
+        </test>
+        <test>
+            <!-- Test2:  80% of bases with quality 20 or higher -->
+            <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/>
+            <param name="quality" value="20"/>
+            <param name="percent" value="80"/>
+            <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool filters reads based on quality scores.
+
+.. class:: infomark
+
+Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value.
+
+.. class:: infomark
+
+Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value.
+
+--------
+
+Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded.
+
+
+**Example**::
+
+    @CSHL_4_FC042AGOOII:1:2:214:584
+    GACAATAAAC
+    +CSHL_4_FC042AGOOII:1:2:214:584
+    30 30 30 30 30 30 30 30 20 10
+
+Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30).
+
+Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30).
+
+Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20).
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq
new file mode 100644
index 00000000000..ea3db077f2e
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out
new file mode 100644
index 00000000000..f274daf1c83
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1a.out
@@ -0,0 +1,4 @@
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out
new file mode 100644
index 00000000000..6353aded69b
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_quality_filter/test-data/fastq_qual_filter1b.out
@@ -0,0 +1,24 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml
new file mode 100644
index 00000000000..09053c5e708
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Convert Formats
+description: FASTQ to FASTA converter
+long_description: |
+  This tool converts data from FASTQ format to FASTA format.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fastq_to_fasta
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml
new file mode 100644
index 00000000000..3af86921661
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml
@@ -0,0 +1,85 @@
+<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1">
+    <description>converter from FASTX-toolkit</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastq_to_fasta
+$SKIPN
+$RENAMESEQ
+-o '$output'
+-v @FQQUAL@
+    ]]></command>
+    <inputs>
+        <expand macro="fastq_input" />
+        <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
+            <option value="">yes</option>
+            <option value="-n">no</option>
+        </param>
+        <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
+            <option value="-r">yes</option>
+            <option value="">no</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- FASTQ-To-FASTA, keep N, don't rename -->
+            <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
+            <param name="SKIPN" value=""/>
+            <param name="RENAMESEQ" value=""/>
+            <output name="output" file="fastq_to_fasta1a.out" />
+        </test>
+        <test>
+            <!-- FASTQ-To-FASTA, discard N, rename -->
+            <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <output name="output" file="fastq_to_fasta1b.out" />
+        </test>
+        <test>
+            <!-- FASTQ-To-FASTA, discard N, rename -->
+            <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <output name="output" file="fastq_to_fasta-out2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool converts data from Solexa format to FASTA format (scroll down for format description).
+
+--------
+
+**Example**
+
+The following data in Solexa-FASTQ format::
+
+    @CSHL_4_FC042GAMMII_2_1_517_596
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    +CSHL_4_FC042GAMMII_2_1_517_596
+    40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+
+Will be converted to FASTA (with 'rename sequence names' = NO)::
+
+    >CSHL_4_FC042GAMMII_2_1_517_596
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+
+Will be converted to FASTA (with 'rename sequence names' = YES)::
+
+    >1
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq
new file mode 100644
index 00000000000..d82412b46e3
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-in2.fastq
@@ -0,0 +1,40 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out
new file mode 100644
index 00000000000..abd084d1577
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta-out2.out
@@ -0,0 +1,20 @@
+>1
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
+>2
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
+>3
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
+>4
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
+>5
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
+>6
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
+>7
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
+>8
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
+>9
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
+>10
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq
new file mode 100644
index 00000000000..d3386dda038
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out
new file mode 100644
index 00000000000..c524fd4e12a
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1a.out
@@ -0,0 +1,16 @@
+>CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+>CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
+>CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+>CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
+>CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+>CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+>CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out
new file mode 100644
index 00000000000..c5b35f433d9
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastq_to_fasta/test-data/fastq_to_fasta1b.out
@@ -0,0 +1,18 @@
+>1
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+>2
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+>3
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+>4
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
+>5
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+>6
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
+>7
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+>8
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+>9
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml
new file mode 100644
index 00000000000..8cbb256861b
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Fastq Manipulation
+description: Remove sequencing artifacts
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+long_description: |
+  This tool filters sequencing artifacts (reads with all but 3 identical bases).
+name: fastx_artifacts_filter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml
new file mode 100644
index 00000000000..d669493ff95
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml
@@ -0,0 +1,92 @@
+<tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_artifacts_filter
+-v
+-o '$output'
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastx_input" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Filter FASTA file -->
+            <param name="input" value="fastx_artifacts1.fasta" />
+            <output name="output" ftype="fasta" file="fastx_artifacts1.out" />
+        </test>
+        <test>
+            <!-- Filter FASTQ file -->
+            <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
+            <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool filters sequencing artifacts (reads with all but 3 identical bases).
+
+--------
+
+**The following is an example of sequences which will be filtered out**::
+
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+    AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
+    AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA
+    AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA
+    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta
new file mode 100644
index 00000000000..bd848fd4b27
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.fasta
@@ -0,0 +1,24 @@
+>CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
+>CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
+>CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
+>CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
+>CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out
new file mode 100644
index 00000000000..77833e34f4d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts1.out
@@ -0,0 +1,14 @@
+>CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
+>CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
+>CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
+>CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq
new file mode 100644
index 00000000000..e3caaf2d9f2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.fastq
@@ -0,0 +1,60 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1601:1525
+AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1601:1525
+40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 12 40 40 30 30 40 40 40 12 36 23 17 24 18 22 25 15 10 34 14
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:1713:528
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++CSHL_3_FC0420AGLLKK:2:1:1713:528
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 12 38 15 22 20 17 14 12 10 7 22 11
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:1236:1157
+AAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1236:1157
+40 40 40 40 40 40 40 40 40 40 40 40 40 35 40 40 40 40 40 33 40 37 40 40 40 18 16 20 23 22 31 26 10 22 19
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
+@CSHL_3_FC0420AGLLKK:2:1:1818:550
+AAAAAAAAAAAAAAAACAAAAACAAAAAAAACAAA
++CSHL_3_FC0420AGLLKK:2:1:1818:550
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 32 40 33 40 40 38 37 40 28 29 27 22 13 20 19 17 17 13 33 18
+@CSHL_3_FC0420AGLLKK:2:1:1764:391
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC0420AGLLKK:2:1:1764:391
+40 40 40 40 40 40 40 40 40 40 40 33 40 40 40 40 40 24 40 40 40 40 40 12 40 24 14 9 22 15 29 18 11 40 22
diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out
new file mode 100644
index 00000000000..d82412b46e3
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/test-data/fastx_artifacts2.out
@@ -0,0 +1,40 @@
+@CSHL_3_FC0420AGLLKK:2:1:233:1674
+GTTAGAGGGAATACACCCACTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:233:1674
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 32 40 40 40 40 16 20 25 9 21 37 40 40 16 29 26 30
+@CSHL_3_FC0420AGLLKK:2:1:136:448
+GTTCTCAGGACCCCTTCAGTAGTNGGCACCATCAA
++CSHL_3_FC0420AGLLKK:2:1:136:448
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -5 13 17 28 40 40 8 17 27 8 13 10
+@CSHL_3_FC0420AGLLKK:2:1:237:1037
+GTGATAGATTGTCTTGTTGTTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:237:1037
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4 40 40 26 35 40 38 40 6 40 40 0 3 26 32 27 14 11 26 11
+@CSHL_3_FC0420AGLLKK:2:1:1805:1464
+GATGCGTTCGAGATGGGTGCGCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1805:1464
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 28 40 21 40 9 37 13 20 21 7 11 14 14 6 23 10
+@CSHL_3_FC0420AGLLKK:2:1:126:1087
+GAGATATTCGAATGCATCATCAGATGGCACCATCA
++CSHL_3_FC0420AGLLKK:2:1:126:1087
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 40 40 40 40 40 31 40 40 11 10 23 40 13 12 17 37 17 22
+@CSHL_3_FC0420AGLLKK:2:1:1488:1323
+GTTTTTTCCCCTAATCTGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:1488:1323
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 22 31 40 40 12 29 22 0 7 12 8 18 7 3 18 9
+@CSHL_3_FC0420AGLLKK:2:1:913:199
+GTTCAGTGTTGGTGCACTGTGTTNTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:913:199
+40 40 39 40 40 40 40 40 40 40 40 40 4 40 40 24 34 20 33 21 36 32 40 -5 40 13 21 21 26 17 18 25 14 25 21
+@CSHL_3_FC0420AGLLKK:2:1:928:765
+GTTTTCAGTTCGAGGTTCGTGCTNTAGGCATTATC
++CSHL_3_FC0420AGLLKK:2:1:928:765
+40 40 40 40 40 40 40 40 40 40 40 40 40 25 27 40 37 35 27 40 40 17 40 -5 36 11 19 15 19 16 11 12 12 23 11
+@CSHL_3_FC0420AGLLKK:2:1:727:1020
+GTAATATAGTTGATAAGAATCTGCAGAGAGAATCA
++CSHL_3_FC0420AGLLKK:2:1:727:1020
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 24 18 38 33 26 16 23 22 16 18
+@CSHL_3_FC0420AGLLKK:2:1:758:1799
+GTAGAGACCCCCTAATAGAGTCTGTAGGCACCATC
++CSHL_3_FC0420AGLLKK:2:1:758:1799
+40 40 40 40 40 40 40 40 35 40 39 40 40 27 20 40 17 34 15 40 40 40 40 15 28 17 4 12 10 10 18 14 3 14 11
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml
new file mode 100644
index 00000000000..adfe8443dab
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Fastq Manipulation
+description: Barcode Splitter
+long_description: |
+  This tool splits a FASTQ file or a regular FASTA file into several files, using barcodes as the split criteria.
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fastx_barcode_splitter
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png b/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png
new file mode 100644
index 00000000000..c0f8944cc8b
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_barcode_splitter/barcode_splitter_output_example.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.pl b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.pl
new file mode 100755
index 00000000000..d08bdb5535c
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.pl
@@ -0,0 +1,571 @@
+#!/usr/bin/env perl
+
+#    FASTX-toolkit - FASTA/FASTQ preprocessing tools.
+#    Copyright (C) 2009-2013  A. Gordon (assafgordon@gmail.com)
+#
+#   Lance Parsons (lparsons@princeton.edu)
+#   3/21/2011 - Modified to accept separate index file for barcodes
+#   4/6/2011 - Modified to cleanup bad barcode identifiers (esp. useful for Galaxy)
+#   4/28/2016 - Modified summary output to remove file paths and add comment
+#               character '#'
+
+#   This program is free software: you can redistribute it and/or modify
+#   it under the terms of the GNU Affero General Public License as
+#   published by the Free Software Foundation, either version 3 of the
+#   License, or (at your option) any later version.
+#
+#   This program is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#   GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+use strict;
+use warnings;
+use IO::Handle;
+use Data::Dumper;
+use Getopt::Long;
+use Carp;
+
+##
+## This program splits a FASTQ/FASTA file into several smaller files,
+## Based on barcode matching.
+##
+## run with "--help" for usage information
+##
+## Assaf Gordon <assafgordon@gmail.com> , 11sep2008
+
+# Forward declarations
+sub load_barcode_file ($);
+sub parse_command_line ;
+sub match_sequences ;
+sub mismatch_count($$) ;
+sub print_results;
+sub open_and_detect_input_format;
+sub open_index_and_detect_input_format($);
+sub read_index_record;
+sub read_record;
+sub write_record($);
+sub usage();
+
+# Global flags and arguments,
+# Set by command line argumens
+my $barcode_file ;
+my $barcodes_at_eol = 0 ;
+my $barcodes_at_bol = 0 ;
+my $index_read_file ;
+my $exact_match = 0 ;
+my $allow_partial_overlap = 0;
+my $allowed_mismatches = 1;
+my $newfile_suffix = '';
+my $newfile_prefix  ;
+my $quiet = 0 ;
+my $debug = 0 ;
+my $fastq_format = 1;
+my $index_fastq_format = 1;
+my $read_id_check_strip_characters = 1;
+
+# Global variables
+# Populated by 'create_output_files'
+my %filenames;
+my %files;
+my %counts = ( 'unmatched' => 0 );
+my $barcodes_length;
+my @barcodes;
+my $input_file_io;
+
+
+# The Four lines per record in FASTQ format.
+# (when using FASTA format, only the first two are used)
+my $seq_name;
+my $seq_bases;
+my $seq_name2;
+my $seq_qualities;
+
+# Values used for index read file
+my $index_seq_name;
+my $index_seq_bases;
+my $index_seq_name2;
+my $index_seq_qualities;
+
+#
+# Start of Program
+#
+parse_command_line ;
+
+load_barcode_file ( $barcode_file ) ;
+
+open_and_detect_input_format;
+
+if (defined $index_read_file) {open_index_and_detect_input_format ( $index_read_file );}
+
+match_sequences ;
+
+print_results unless $quiet;
+
+#
+# End of program
+#
+
+sub parse_command_line {
+    my $help;
+
+    usage() if (scalar @ARGV==0);
+
+    my $result = GetOptions ( "bcfile=s" => \$barcode_file,
+                  "eol"  => \$barcodes_at_eol,
+                  "bol"  => \$barcodes_at_bol,
+                  "idxfile=s"  => \$index_read_file,
+                  "idxidstrip=i" => \$read_id_check_strip_characters,
+                  "exact" => \$exact_match,
+                  "prefix=s" => \$newfile_prefix,
+                  "suffix=s" => \$newfile_suffix,
+                  "quiet" => \$quiet,
+                  "partial=i" => \$allow_partial_overlap,
+                  "debug" => \$debug,
+                  "mismatches=i" => \$allowed_mismatches,
+                  "help" => \$help
+    ) ;
+
+    usage() if ($help);
+
+    die "Error: barcode file not specified (use '--bcfile [FILENAME]')\n" unless defined $barcode_file;
+    die "Error: prefix path/filename not specified (use '--prefix [PATH]')\n" unless defined $newfile_prefix;
+
+    if (! defined $index_read_file) {
+        if ($barcodes_at_bol == $barcodes_at_eol) {
+            die "Error: can't specify both --eol & --bol\n" if $barcodes_at_eol;
+            die "Error: must specify either --eol or --bol or --idxfile\n" ;
+        }
+    }
+    elsif ($barcodes_at_bol || $barcodes_at_eol) {
+        die "Error: Must specify only one of --idxfile, --eol, or --bol";
+    }
+
+    die "Error: invalid for value partial matches (valid values are 0 or greater)\n" if $allow_partial_overlap<0;
+
+    $allowed_mismatches = 0 if $exact_match;
+
+    die "Error: invalid value for mismatches (valid values are 0 or more)\n" if ($allowed_mismatches<0);
+
+    die "Error: partial overlap value ($allow_partial_overlap) bigger than " .
+        "max. allowed mismatches ($allowed_mismatches)\n" if ($allow_partial_overlap > $allowed_mismatches);
+
+
+    exit unless $result;
+}
+
+
+
+#
+# Read the barcode file
+#
+sub load_barcode_file ($) {
+    my $filename = shift or croak "Missing barcode file name";
+
+    open BCFILE,"<$filename" or die "Error: failed to open barcode file ($filename)\n";
+    while (<BCFILE>) {
+        next if m/^#/;
+        chomp;
+        my ($ident, $barcode) = split('\t') ;
+
+        $barcode = uc($barcode);
+
+        # Sanity checks on the barcodes
+        die "Error: bad data at barcode file ($filename) line $.\n" unless defined $barcode;
+        die "Error: bad barcode value ($barcode) at barcode file ($filename) line $.\n"
+            unless $barcode =~ m/^[AGCT]+$/;
+
+        # Cleanup Identifiers (only allow alphanumeric, replace others with dash '-')
+        $ident =~ s/[^A-Za-z0-9]/-/g;
+        die "Error: bad identifier value ($ident) at barcode file ($filename) line $. (must be alphanumeric)\n"
+            unless $ident =~ m/^\w+$/;
+
+        die "Error: badcode($ident, $barcode) is shorter or equal to maximum number of " .
+            "mismatches ($allowed_mismatches). This makes no sense. Specify fewer mismatches.\n"
+                if length($barcode)<=$allowed_mismatches;
+
+        $barcodes_length = length($barcode) unless defined $barcodes_length;
+        die "Error: found barcodes in different lengths. this feature is not supported yet.\n"
+            unless $barcodes_length == length($barcode);
+
+        push @barcodes, [$ident, $barcode];
+
+        if ($allow_partial_overlap>0) {
+            foreach my $i (1 .. $allow_partial_overlap) {
+                substr $barcode, ($barcodes_at_bol)?0:-1, 1, '';
+                push @barcodes, [$ident, $barcode];
+            }
+        }
+    }
+    close BCFILE;
+
+    if ($debug) {
+        print STDERR "barcode\tsequence\n";
+        foreach my $barcoderef (@barcodes) {
+            my ($ident, $seq) = @{$barcoderef};
+            print STDERR $ident,"\t", $seq ,"\n";
+        }
+    }
+}
+
+# Create one output file for each barcode.
+# (Also create a file for the dummy 'unmatched' barcode)
+sub create_output_files {
+    my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers;
+    $barcodes{'unmatched'} = 1 ;
+
+    foreach my $ident (keys %barcodes) {
+        my $new_filename = $newfile_prefix . $ident . $newfile_suffix;
+        $filenames{$ident} = $new_filename;
+        open my $file, ">$new_filename" or die "Error: failed to create output file ($new_filename)\n";
+        $files{$ident} = $file ;
+    }
+}
+
+sub match_sequences {
+
+    my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers;
+    $barcodes{'unmatched'} = 1 ;
+
+    #reset counters
+    foreach my $ident ( keys %barcodes ) {
+        $counts{$ident} = 0;
+    }
+
+    create_output_files;
+
+    # Read file FASTQ file
+    # split accotding to barcodes
+    while ( read_record ) {
+        chomp $seq_name;
+        chomp $seq_bases;
+        if (defined $index_read_file) {
+            read_index_record() or die "Error: Unable to read index sequence for sequence name ($seq_name), check to make sure the file lengths match.\n";
+            chomp $index_seq_name;
+            chomp $index_seq_bases;
+
+            # Assert that the read ids match
+            my $seq_name_match = &strip_read_id($seq_name);
+            my $index_seq_name_match = &strip_read_id($index_seq_name);
+            if ($seq_name_match ne $index_seq_name_match) {
+                die "Error: Index sequence name ($index_seq_name) does not match sequence name ($seq_name)\n";
+            }
+
+        }
+
+        print STDERR "sequence $seq_bases: \n" if $debug;
+
+        my $best_barcode_mismatches_count = $barcodes_length;
+        my $best_barcode_ident = undef;
+
+        #Try all barcodes, find the one with the lowest mismatch count
+        foreach my $barcoderef (@barcodes) {
+            my ($ident, $barcode) = @{$barcoderef};
+
+            # Get DNA fragment (in the length of the barcodes)
+            # The barcode will be tested only against this fragment
+            # (no point in testing the barcode against the whole sequence)
+            my $sequence_fragment;
+            if ($barcodes_at_bol) {
+                $sequence_fragment = substr $seq_bases, 0, $barcodes_length;
+            } elsif ($barcodes_at_eol) {
+                $sequence_fragment = substr $seq_bases, - $barcodes_length;
+            } else {
+                $sequence_fragment = substr $index_seq_bases, 0, $barcodes_length;
+            }
+
+            my $mm = mismatch_count($sequence_fragment, $barcode) ;
+
+            # if this is a partial match, add the non-overlap as a mismatch
+            # (partial barcodes are shorter than the length of the original barcodes)
+            $mm += ($barcodes_length - length($barcode));
+
+            if ( $mm < $best_barcode_mismatches_count ) {
+                $best_barcode_mismatches_count = $mm ;
+                $best_barcode_ident = $ident ;
+            }
+        }
+
+        $best_barcode_ident = 'unmatched'
+            if ( (!defined $best_barcode_ident) || $best_barcode_mismatches_count>$allowed_mismatches) ;
+
+        print STDERR "sequence $seq_bases matched barcode: $best_barcode_ident\n" if $debug;
+
+        $counts{$best_barcode_ident}++;
+
+        #get the file associated with the matched barcode.
+        #(note: there's also a file associated with 'unmatched' barcode)
+        my $file = $files{$best_barcode_ident};
+
+        write_record($file);
+    }
+}
+
+# Strip end of readids when matching to avoid mismatch between read 1, 2, 3, etc.
+sub strip_read_id {
+    my $read_id = shift;
+    my $stripped_read_id = $read_id;
+    if ($read_id_check_strip_characters) {
+        if ($read_id =~ /@([^:]+):([0-9]+):([^:]+):([0-9]+):([0-9]+):([0-9]+):([0-9]+) ([0-9]+):([YN]):([0-9]+):([ACGT]+){0,1}/) { # CASAVA 1.8+
+            my @parts = split(/ /,$read_id);
+            $stripped_read_id = $parts[0];
+        } else { # CASAVA 1.7 and earlier
+            $stripped_read_id = substr($read_id, 0, length($read_id)-$read_id_check_strip_characters);
+        }
+    }
+    return $stripped_read_id;
+}
+
+#Quickly calculate hamming distance between two strings
+#
+#NOTE: Strings must be same length.
+#      returns number of different characters.
+#see  http://www.perlmonks.org/?node_id=500235
+sub mismatch_count($$) { length( $_[ 0 ] ) - ( ( $_[ 0 ] ^ $_[ 1 ] ) =~ tr[\0][\0] ) }
+
+sub print_results
+{
+    print "# Barcode\tCount\n";
+    my $total = 0 ;
+    foreach my $ident (sort keys %counts) {
+        print $ident, "\t", $counts{$ident},"\n";
+        $total += $counts{$ident};
+    }
+    print "total\t",$total,"\n";
+}
+
+sub read_record
+{
+    $seq_name = $input_file_io->getline();
+
+    return undef unless defined $seq_name; # End of file?
+
+    $seq_bases = $input_file_io->getline();
+    die "Error: bad input file, expecting line with sequences\n" unless defined $seq_bases;
+
+    # If using FASTQ format, read two more lines
+    if ($fastq_format) {
+        $seq_name2 = $input_file_io->getline();
+        die "Error: bad input file, expecting line with sequence name2\n" unless defined $seq_name2;
+
+        $seq_qualities = $input_file_io->getline();
+        die "Error: bad input file, expecting line with quality scores\n" unless defined $seq_qualities;
+    }
+    return 1;
+}
+
+sub write_record($)
+{
+    my $file = shift;
+
+    croak "Bad file handle" unless defined $file;
+
+    print $file $seq_name,"\n";
+    print $file $seq_bases,"\n";
+
+    #if using FASTQ format, write two more lines
+    if ($fastq_format) {
+        print $file $seq_name2;
+        print $file $seq_qualities;
+    }
+}
+
+sub open_and_detect_input_format
+{
+    $input_file_io = new IO::Handle;
+    die "Failed to open STDIN " unless $input_file_io->fdopen(fileno(STDIN),"r");
+
+    # Get the first characeter, and push it back
+    my $first_char = $input_file_io->getc();
+    $input_file_io->ungetc(ord $first_char);
+
+    if ($first_char eq '>') {
+        # FASTA format
+        $fastq_format = 0 ;
+        print STDERR "Detected FASTA format\n" if $debug;
+    } elsif ($first_char eq '@') {
+        # FASTQ format
+        $fastq_format = 1;
+        print STDERR "Detected FASTQ format\n" if $debug;
+    } else {
+        die "Error: unknown file format. First character = '$first_char' (expecting > or \@)\n";
+    }
+}
+
+sub open_index_and_detect_input_format($) {
+    my $filename = shift or croak "Missing index read file name";
+
+    open IDXFILE,"<$filename" or die "Error: failed to open index read file ($filename)\n";
+
+    # Get the first line, and reset file pointer
+    my $first_line = <IDXFILE>;
+    my $first_char = substr($first_line, 0, 1);
+    seek(IDXFILE, 0, 0);
+
+    if ($first_char eq '>') {
+        # FASTA format
+        $index_fastq_format = 0 ;
+        print STDERR "Detected FASTA format for index file\n" if $debug;
+    } elsif ($first_char eq '@') {
+        # FASTQ format
+        $index_fastq_format = 1;
+        print STDERR "Detected FASTQ format for index file\n" if $debug;
+    } else {
+        die "Error: unknown index file format. First character = '$first_char' (expecting > or \@)\n";
+    }
+}
+
+sub read_index_record
+{
+    $index_seq_name = <IDXFILE>;
+
+    return undef unless defined $index_seq_name; # End of file?
+
+    $index_seq_bases = <IDXFILE>;
+    die "Error: bad input file, expecting line with sequences\n" unless defined $index_seq_bases;
+
+    # If using FASTQ format, read two more lines
+    if ($index_fastq_format) {
+        $index_seq_name2    = <IDXFILE>;
+        die "Error: bad input file, expecting line with sequence name2\n" unless defined $index_seq_name2;
+
+        $index_seq_qualities = <IDXFILE>;
+        die "Error: bad input file, expecting line with quality scores\n" unless defined $index_seq_qualities;
+    }
+    return 1;
+}
+
+sub usage()
+{
+    print<<EOF;
+Barcode Splitter, by Assaf Gordon (gordon\@cshl.edu), 11sep2008
+
+This program reads FASTA/FASTQ file and splits it into several smaller files,
+Based on barcode matching.
+FASTA/FASTQ data is read from STDIN (format is auto-detected.)
+Output files will be writen to disk.
+Summary will be printed to STDOUT.
+
+usage: $0 --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol|--eol|--idxfile]
+         [--mismatches N] [--exact] [--partial N] [--idxidstrip N]
+         [--help] [--quiet] [--debug]
+
+Arguments:
+
+--bcfile FILE  - Barcodes file name. (see explanation below.)
+--prefix PREFIX  - File prefix. will be added to the output files. Can be used
+      to specify output directories.
+--suffix SUFFIX  - File suffix (optional). Can be used to specify file
+      extensions.
+--bol    - Try to match barcodes at the BEGINNING of sequences.
+      (What biologists would call the 5' end, and programmers
+      would call index 0.)
+--eol    - Try to match barcodes at the END of sequences.
+      (What biologists would call the 3' end, and programmers
+      would call the end of the string.)
+--idxfile FILE  - Read barcodes from separate index file (fasta or fastq)
+      NOTE: one of --bol, --eol, --idxfile must be specified,
+           but not more than one.
+--idxidstrip N  - When using index file, strip this number of characters
+      from the end of the sequence id before matching.
+      Automatically detects CASAVA 1.8 format and strips at a
+      space in the id, use 0 to disable this.
+      (Default is 1).
+--mismatches N  - Max. number of mismatches allowed. default is 1.
+--exact    - Same as '--mismatches 0'. If both --exact and --mismatches
+      are specified, '--exact' takes precedence.
+--partial N  - Allow partial overlap of barcodes. (see explanation below.)
+      (Default is not partial matching)
+--quiet    - Don't print counts and summary at the end of the run.
+      (Default is to print.)
+--debug    - Print lots of useless debug information to STDERR.
+--help    - This helpful help screen.
+
+Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is
+the barcodes file):
+
+  \$ cat s_2_100.txt | $0 --bcfile mybarcodes.txt --bol --mismatches 2 \\
+  --prefix /tmp/bla_ --suffix ".txt"
+
+Barcode file format
+-------------------
+Barcode files are simple text files. Each line should contain an identifier
+(descriptive name for the barcode), and the barcode itself (A/C/G/T),
+separated by a TAB character. Example:
+
+    #This line is a comment (starts with a 'number' sign)
+    BC1 GATCT
+    BC2 ATCGT
+    BC3 GTGAT
+    BC4 TGTCT
+
+For each barcode, a new FASTQ file will be created (with the barcode's
+identifier as part of the file name). Sequences matching the barcode
+will be stored in the appropriate file.
+
+Running the above example (assuming "mybarcodes.txt" contains the above
+barcodes), will create the following files:
+  /tmp/bla_BC1.txt
+  /tmp/bla_BC2.txt
+  /tmp/bla_BC3.txt
+  /tmp/bla_BC4.txt
+  /tmp/bla_unmatched.txt
+The 'unmatched' file will contain all sequences that didn't match any barcode.
+
+Barcode matching
+----------------
+
+** Without partial matching:
+
+Count mismatches between the FASTA/Q sequences and the barcodes.
+The barcode which matched with the lowest mismatches count (providing the
+count is small or equal to '--mismatches N') 'gets' the sequences.
+
+Example (using the above barcodes):
+Input Sequence:
+GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
+
+Matching with '--bol --mismatches 1':
+GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
+GATCT (1 mismatch, BC1)
+ATCGT (4 mismatches, BC2)
+GTGAT (3 mismatches, BC3)
+TGTCT (3 mismatches, BC4)
+
+This sequence will be classified as 'BC1' (it has the lowest mismatch count).
+If '--exact' or '--mismatches 0' were specified, this sequence would be
+classified as 'unmatched' (because, although BC1 had the lowest mismatch count,
+it is above the maximum allowed mismatches).
+
+Matching with '--eol' (end of line) does the same, but from the other side
+of the sequence.
+
+** With partial matching (very similar to indels):
+
+Same as above, with the following addition: barcodes are also checked for
+partial overlap (number of allowed non-overlapping bases is '--partial N').
+
+Example:
+Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
+(Same as above, but note the missing 'G' at the beginning.)
+
+Matching (without partial overlapping) against BC1 yields 4 mismatches:
+ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
+GATCT (4 mismatches)
+
+Partial overlapping would also try the following match:
+-ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
+GATCT (1 mismatch)
+
+Note: scoring counts a missing base as a mismatch, so the final
+mismatch count is 2 (1 'real' mismatch, 1 'missing base' mismatch).
+If running with '--mismatches 2' (meaning allowing upto 2 mismatches) - this
+seqeunce will be classified as BC1.
+
+EOF
+
+exit 1;
+}
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml
new file mode 100644
index 00000000000..cbb64975b48
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml
@@ -0,0 +1,129 @@
+<tool id="cshl_fastx_barcode_splitter" version="1.0.1" name="Barcode Splitter">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+mkdir split &&
+@CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
+--prefix 'split/'
+--suffix '.$input.extension'
+--mismatches $mismatches
+--partial $partial
+#if $refBarcodeLocation.barcodeLocation == "idxfile":
+    --idxfile '$refBarcodeLocation.idxfile'
+    --idxidstrip $refBarcodeLocation.idxidstrip
+#else:
+    $refBarcodeLocation.EOL
+#end if
+> '$summary'
+    ]]></command>
+    <inputs>
+        <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
+        <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" />
+
+        <conditional name="refBarcodeLocation">
+            <param name="barcodeLocation" type="select" label="Barcodes found at">
+                <option value="bol">Start of sequence (5' end)</option>
+                <option value="eol">End of sequence (3' end)</option>
+                <option value="idxfile">Separate index file</option>
+            </param>
+            <when value="bol">
+                <param name="EOL" type="hidden" value="--bol" />
+            </when>
+            <when value="eol">
+                <param name="EOL" type="hidden" value="--eol" />
+            </when>
+            <when value="idxfile">
+                <param argument="--idxidstrip" type="integer" value="1" label="Characters to strip from the end of the sequence id before matching" />
+                <param argument="--idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
+            </when>
+        </conditional>
+        <param argument="--mismatches" type="integer" value="0" label="Number of allowed mismatches" />
+        <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
+    </inputs>
+
+    <outputs>
+        <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
+        <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
+        </collection>
+    </outputs>
+
+    <tests>
+        <test>
+            <!-- Split a FASTQ file -->
+            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+            <param name="barcodeLocation" value="bol" />
+            <param name="mismatches" value="2" />
+            <param name="partial" value="0" />
+            <output name="summary" file="fastx_barcode_splitter1.out" />
+            <output_collection name="split_output" type="list">
+                <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+                <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+                <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+                <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+                <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+            </output_collection>
+        </test>
+
+        <test>
+            <!-- Split a FASTQ file, using separate index read -->
+            <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+            <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+            <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
+            <param name="barcodeLocation" value="idxfile" />
+            <param name="mismatches" value="2" />
+            <param name="partial" value="0" />
+            <output name="summary" file="fastx_barcode_splitter1.out" />
+            <output_collection name="split_output" type="list">
+                <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+                <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+                <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+                <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+                <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+            </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
+
+--------
+
+**Barcode file Format**
+
+Barcode files are simple text files.
+Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
+Example::
+
+    #This line is a comment (starts with a 'number' sign)
+    BC1    GATCT
+    BC2    ATCGT
+    BC3    GTGAT
+    BC4 TGTCT
+
+For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
+Sequences matching the barcode will be stored in the appropriate file.
+
+One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
+
+The output of this tool is an HTML file, displaying the split counts and the file locations.
+
+**Output Example**
+
+.. image:: barcode_splitter_output_example.png
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq
new file mode 100644
index 00000000000..f1afc9660d4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.fastq
@@ -0,0 +1,168 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out
new file mode 100644
index 00000000000..bb704378ef5
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.out
@@ -0,0 +1,7 @@
+# Barcode	Count
+BC1	11
+BC2	12
+BC3	9
+BC4	1
+unmatched	9
+total	42
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt
new file mode 100644
index 00000000000..8a7ba617b8d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1.txt
@@ -0,0 +1,4 @@
+BC1	GATCT
+BC2	ATCGT
+BC3	GTGAT
+BC4	TGTCT
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out
new file mode 100644
index 00000000000..e512d0d4ff4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC1.out
@@ -0,0 +1,44 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTAGTAGTAGTAGA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out
new file mode 100644
index 00000000000..85732c3d098
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC2.out
@@ -0,0 +1,48 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTCGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out
new file mode 100644
index 00000000000..9780da92424
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC3.out
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAATGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out
new file mode 100644
index 00000000000..4ea8151b368
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_BC4.out
@@ -0,0 +1,4 @@
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+TGTCTGAGTATACACAT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out
new file mode 100644
index 00000000000..6dd823f33a8
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter1_unmatched.out
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTACGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTTGAGTATACACAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaa
+@CSHL_3_FC042AGLLWW:1:2:7:203/1
+TAGTTTCTCTATGTACA
++CSHL_3_FC042AGLLWW:1:2:7:203/1
+aab^V^aU]`aa^aZaa
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq
new file mode 100644
index 00000000000..10adf673908
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/test-data/fastx_barcode_splitter_index.fastq
@@ -0,0 +1,168 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GATCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTCT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGTAC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCGT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+ATCTC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GGAAT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V
+@CSHL_3_FC042AGLLWW:1:2:7:203/2
+TAGTT
++CSHL_3_FC042AGLLWW:1:2:7:203/2
+aab^V
+@HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+TGTCT
++HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0:
+aab^V
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml
new file mode 100644
index 00000000000..ec81cc34586
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Fastq Manipulation
+description: Clip adapter sequences
+long_description: |
+  This tool clips adapters from the 3''-end of the sequences in a FASTA/FASTQ file.
+name: fastx_clipper
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml
new file mode 100644
index 00000000000..c42242c5648
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml
@@ -0,0 +1,104 @@
+<tool id="cshl_fastx_clipper" name="Clip" version="1.0.2">
+    <description>adapter sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_clipper
+-l $minlength
+-a '$clip_source.clip_sequence'
+-d $keepdelta
+-o '$output'
+-v
+$KEEP_N
+$DISCARD_OPTIONS
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastx_input" />
+
+        <param name="minlength" type="integer" value="15"
+            label="Minimum sequence length (after clipping, sequences shorter than this length will be discarded" />
+
+        <conditional name="clip_source">
+            <param name="clip_source_list" type="select" label="Source">
+                <option value="prebuilt" selected="true">Standard (select from the list below)</option>
+                <option value="user">Enter custom sequence</option>
+            </param>
+
+            <when value="user">
+                <param name="clip_sequence" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
+            </when>
+
+            <when value="prebuilt">
+                <param name="clip_sequence" type="select" label="Choose Adapter">
+                    <options from_file="fastx_clipper_sequences.txt">
+                        <column name="name" index="1"/>
+                        <column name="value" index="0"/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
+
+        <param name="keepdelta" type="integer" value="0"
+            label="Enter a non-zero value to keep the adapter sequence and x bases that follow it"
+            help="Use this for hairpin barcoding. keep at 0 unless you know what you're doing" />
+
+        <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
+            <option value="">Yes</option>
+            <option value="-n">No</option>
+        </param>
+
+        <param name="DISCARD_OPTIONS" type="select" label="Output options">
+            <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
+            <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
+            <option value="">Output both clipped and non-clipped sequences</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
+            <param name="maxmismatches" value="2" />
+            <param name="minlength" value="15" />
+            <param name="clip_source_list" value="user" />
+            <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
+            <param name="keepdelta" value="0" />
+            <param name="KEEP_N" value="-n" />
+            <param name="DISCARD_OPTIONS" value="-c" />
+            <output name="output" ftype="fastqsolexa" file="fastx_clipper1a.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
+
+--------
+
+
+**Clipping Illustration:**
+
+.. image:: fastx_clipper_illustration.png
+
+**Clipping Example:**
+
+.. image:: fastx_clipper_example.png
+
+**In the above example:**
+
+* Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
+* Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png
new file mode 100644
index 00000000000..d04d629d548
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_example.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_illustration.png b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_illustration.png
new file mode 100644
index 00000000000..5acf892fac9
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper_illustration.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/macros.xml b/tool_collections/fastx_toolkit/fastx_clipper/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1.fastq b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1.fastq
new file mode 100644
index 00000000000..d3386dda038
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out
new file mode 100644
index 00000000000..9a52a29fe49
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/test-data/fastx_clipper1a.out
@@ -0,0 +1,8 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATG
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabb
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample
new file mode 100644
index 00000000000..79f88f1c3a7
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/tool-data/fastx_clipper_sequences.txt.sample
@@ -0,0 +1,13 @@
+#
+# Adapter/Linker sequences for FASTX-Clipper tool.
+#
+# Format:
+#    Adapter Sequence <TAB> Descriptive name
+#
+# Example:
+#     AAATTTGATAAGATA   Our-Adapter
+#
+# Some adapters can be found here:
+# http://seqanswers.com/forums/showthread.php?t=198
+#
+#TGTAGGCC	Dummy-Adapter (don't use me)
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml
new file mode 100644
index 00000000000..1bb65f07db4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_collapser/.shed.yml
@@ -0,0 +1,10 @@
+categories:
+- Fasta Manipulation
+description: Collapse sequences
+long_description: |
+  This tool collapses identical sequences in a FASTA file into a single sequence.
+name: fastx_collapser
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml
new file mode 100644
index 00000000000..5c7302e5510
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml
@@ -0,0 +1,88 @@
+<tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse">
+    <description>sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_collapser -v
+-o '$output'
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastx_input" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fasta_collapser1.fasta" />
+            <!-- The output is sorted differently depending on architecture,
+                 so the sort attribute is needed here -->
+            <output name="output" file="fasta_collapser1.out" sort="true" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool collapses identical sequences in a FASTA file into a single sequence.
+
+--------
+
+**Example**
+
+Example Input File (Sequence "ATAT" appears multiple times)::
+
+    >CSHL_2_FC0042AGLLOO_1_1_605_414
+    TGCG
+    >CSHL_2_FC0042AGLLOO_1_1_537_759
+    ATAT
+    >CSHL_2_FC0042AGLLOO_1_1_774_520
+    TGGC
+    >CSHL_2_FC0042AGLLOO_1_1_742_502
+    ATAT
+    >CSHL_2_FC0042AGLLOO_1_1_781_514
+    TGAG
+    >CSHL_2_FC0042AGLLOO_1_1_757_487
+    TTCA
+    >CSHL_2_FC0042AGLLOO_1_1_903_769
+    ATAT
+    >CSHL_2_FC0042AGLLOO_1_1_724_499
+    ATAT
+
+Example Output file::
+
+    >1-1
+    TGCG
+    >2-4
+    ATAT
+    >3-1
+    TGGC
+    >4-1
+    TGAG
+    >5-1
+    TTCA
+
+.. class:: infomark
+
+Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.
+
+The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.
+
+The following output::
+
+    >2-4
+    ATAT
+
+means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/macros.xml b/tool_collections/fastx_toolkit/fastx_collapser/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_collapser/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta
new file mode 100644
index 00000000000..6720c254408
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.fasta
@@ -0,0 +1,84 @@
+>1
+TGTATTTACAATGACTAGAAA
+>2
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>3
+AGTACAAGGACATGC
+>4
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>5
+AGTACAAGGACATGC
+>6
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>7
+AGTACAAGGACATGC
+>8
+AGTACAAGGACATGC
+>9
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>10
+AGTACAAGGACATGC
+>11
+AGTACAAGGACATGC
+>12
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>13
+CGATTGCCGAAGTCTACCA
+>14
+AGTACAAGGACATGC
+>15
+CCTTGTAGTGGATTCTGATGA
+>16
+AGTACAAGGACATGC
+>17
+AGTACAAGGACATGC
+>18
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>19
+AGTACAAGGACATGC
+>20
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>21
+AGTACAAGGACATGC
+>22
+AGTACAAGGACATGC
+>23
+CTGCTGCGATCGGTGTGC
+>24
+AGTACAAGGACATGC
+>25
+ACCATTCGAGCATAC
+>26
+AGTACAAGGACATGC
+>27
+TCAAATTCTAGATTTTTACGG
+>28
+AGTACAAGGACATGC
+>29
+TGATTTCCAGAGCCAAT
+>30
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>31
+TTACCTCACGATATTGTAATA
+>32
+ATGACTTCATCGTCCACCCTTTAGAACT
+>33
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>34
+TTCAACGCCGCCGTGAAC
+>35
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>36
+CTGCTGCGATCGGTGTGC
+>37
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>38
+TTCAACGCCGCCGTGAAC
+>39
+TTCAACGCCGCCGTGAAC
+>40
+CTGCTGCGATCGGTGTGC
+>41
+TTCAACGCCGCCGTGAAC
+>42
+TTCAACGCCGCCGTGAAC
diff --git a/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out
new file mode 100644
index 00000000000..22f9d963491
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_collapser/test-data/fasta_collapser1.out
@@ -0,0 +1,24 @@
+>1-15
+AGTACAAGGACATGC
+>2-11
+ATTGCTGCTCGGATGGTCCGGCTGTGCACAC
+>3-5
+TTCAACGCCGCCGTGAAC
+>4-3
+CTGCTGCGATCGGTGTGC
+>5-1
+ACCATTCGAGCATAC
+>6-1
+TGTATTTACAATGACTAGAAA
+>7-1
+TGATTTCCAGAGCCAAT
+>8-1
+CGATTGCCGAAGTCTACCA
+>9-1
+TCAAATTCTAGATTTTTACGG
+>10-1
+TTACCTCACGATATTGTAATA
+>11-1
+CCTTGTAGTGGATTCTGATGA
+>12-1
+ATGACTTCATCGTCCACCCTTTAGAACT
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml
new file mode 100644
index 00000000000..5681a673853
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fastq Manipulation
+- Graphics
+description: Draw nucleotides distribution chart
+long_description: |
+  Creates a stacked-histogram graph for the nucleotide distribution in the FASTQ library.
+name: fastx_nucleotides_distribution
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_1.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_1.png
new file mode 100644
index 00000000000..5727acd65c0
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_1.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_2.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_2.png
new file mode 100644
index 00000000000..cdc52a9c80b
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_2.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_3.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_3.png
new file mode 100644
index 00000000000..39d679657ec
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_3.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_4.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_4.png
new file mode 100644
index 00000000000..c6ab9b41660
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastq_nucleotides_distribution_4.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml
new file mode 100644
index 00000000000..ce3c093ec1d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml
@@ -0,0 +1,62 @@
+<tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+fastx_nucleotide_distribution_graph.sh
+-t '$input.name'
+-i '$input'
+-o '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" />
+    </inputs>
+    <outputs>
+        <data name="output" format="png" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastx_nucleotides_distribution-in1.txt" />
+            <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
+
+.. class:: infomark
+
+**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
+
+-----
+
+**Output Examples**
+
+The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
+
+.. image:: fastq_nucleotides_distribution_1.png
+
+In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
+
+.. image:: fastq_nucleotides_distribution_2.png
+
+The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
+
+.. image:: fastq_nucleotides_distribution_3.png
+
+But most of the time, the chart will look rather random:
+
+.. image:: fastq_nucleotides_distribution_4.png
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+    <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out
new file mode 100644
index 00000000000..852c8122efe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out
@@ -0,0 +1,37 @@
+column	count	min	max	sum	mean	Q1	med	Q3	IQR	lW	rW	A_Count	C_Count	G_Count	T_Count	N_Count	Max_count
+1	9	23	34	288	32.00	33	33	33	0	33	33	3	1	4	1	0	9
+2	9	28	33	287	31.89	31	33	33	2	28	33	3	3	2	1	0	9
+3	9	13	34	268	29.78	28	33	33	5	21	34	5	1	0	3	0	9
+4	9	17	33	261	29.00	30	33	33	3	26	33	1	2	3	3	0	9
+5	9	22	33	269	29.89	30	33	33	3	26	33	3	3	3	0	0	9
+6	9	22	33	277	30.78	30	33	33	3	26	33	5	3	0	1	0	9
+7	9	21	33	258	28.67	24	33	33	9	21	33	4	1	3	1	0	9
+8	9	12	33	263	29.22	32	33	33	1	31	33	2	1	1	5	0	9
+9	9	29	33	290	32.22	33	33	33	0	33	33	3	3	2	1	0	9
+10	9	23	33	277	30.78	32	33	33	1	31	33	1	4	2	2	0	9
+11	9	12	33	245	27.22	21	31	33	12	12	33	5	2	1	1	0	9
+12	9	13	33	214	23.78	15	24	33	18	13	33	2	4	2	1	0	9
+13	9	5	33	249	27.67	29	31	33	4	23	33	2	1	1	5	0	9
+14	9	5	33	233	25.89	24	33	33	9	11	33	3	3	2	1	0	9
+15	9	15	33	251	27.89	24	33	33	9	15	33	5	1	1	2	0	9
+16	9	23	34	269	29.89	24	33	33	9	23	34	3	1	2	3	0	9
+17	9	13	34	266	29.56	33	33	33	0	33	33	2	3	1	3	0	9
+18	9	21	34	272	30.22	31	33	33	2	28	34	0	5	1	3	0	9
+19	9	5	34	244	27.11	27	30	33	6	18	34	4	4	1	0	0	9
+20	9	11	34	241	26.78	23	32	33	10	11	34	3	4	2	0	0	9
+21	9	13	33	240	26.67	24	27	33	9	13	33	1	4	0	4	0	9
+22	9	5	33	190	21.11	13	21	33	20	5	33	1	4	0	3	1	9
+23	9	5	33	205	22.78	16	26	33	17	5	33	4	4	1	0	0	9
+24	9	5	33	247	27.44	28	31	33	5	21	33	1	5	1	2	0	9
+25	9	11	34	241	26.78	24	33	33	9	11	34	3	4	0	2	0	9
+26	9	5	33	212	23.56	18	31	33	15	5	33	0	6	0	3	0	9
+27	9	5	33	227	25.22	21	26	33	12	5	33	3	4	1	1	0	9
+28	9	21	33	255	28.33	24	31	33	9	21	33	2	4	3	0	0	9
+29	9	5	33	228	25.33	21	30	33	12	5	33	2	4	1	2	0	9
+30	9	10	33	213	23.67	16	28	33	17	10	33	3	4	2	0	0	9
+31	9	5	33	236	26.22	21	31	33	12	5	33	1	4	1	3	0	9
+32	9	5	33	210	23.33	12	29	33	21	5	33	3	3	0	3	0	9
+33	9	5	33	183	20.33	9	21	33	24	5	33	1	4	2	2	0	9
+34	9	5	33	150	16.67	7	17	22	15	5	33	3	4	1	1	0	9
+35	9	13	33	217	24.11	21	24	29	8	13	33	1	4	1	3	0	9
+36	9	5	33	195	21.67	18	21	32	14	5	33	3	2	1	3	0	9
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nt_distribution.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nt_distribution.png
new file mode 100644
index 00000000000..7dc745a6533
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nt_distribution.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt
new file mode 100644
index 00000000000..852c8122efe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-in1.txt
@@ -0,0 +1,37 @@
+column	count	min	max	sum	mean	Q1	med	Q3	IQR	lW	rW	A_Count	C_Count	G_Count	T_Count	N_Count	Max_count
+1	9	23	34	288	32.00	33	33	33	0	33	33	3	1	4	1	0	9
+2	9	28	33	287	31.89	31	33	33	2	28	33	3	3	2	1	0	9
+3	9	13	34	268	29.78	28	33	33	5	21	34	5	1	0	3	0	9
+4	9	17	33	261	29.00	30	33	33	3	26	33	1	2	3	3	0	9
+5	9	22	33	269	29.89	30	33	33	3	26	33	3	3	3	0	0	9
+6	9	22	33	277	30.78	30	33	33	3	26	33	5	3	0	1	0	9
+7	9	21	33	258	28.67	24	33	33	9	21	33	4	1	3	1	0	9
+8	9	12	33	263	29.22	32	33	33	1	31	33	2	1	1	5	0	9
+9	9	29	33	290	32.22	33	33	33	0	33	33	3	3	2	1	0	9
+10	9	23	33	277	30.78	32	33	33	1	31	33	1	4	2	2	0	9
+11	9	12	33	245	27.22	21	31	33	12	12	33	5	2	1	1	0	9
+12	9	13	33	214	23.78	15	24	33	18	13	33	2	4	2	1	0	9
+13	9	5	33	249	27.67	29	31	33	4	23	33	2	1	1	5	0	9
+14	9	5	33	233	25.89	24	33	33	9	11	33	3	3	2	1	0	9
+15	9	15	33	251	27.89	24	33	33	9	15	33	5	1	1	2	0	9
+16	9	23	34	269	29.89	24	33	33	9	23	34	3	1	2	3	0	9
+17	9	13	34	266	29.56	33	33	33	0	33	33	2	3	1	3	0	9
+18	9	21	34	272	30.22	31	33	33	2	28	34	0	5	1	3	0	9
+19	9	5	34	244	27.11	27	30	33	6	18	34	4	4	1	0	0	9
+20	9	11	34	241	26.78	23	32	33	10	11	34	3	4	2	0	0	9
+21	9	13	33	240	26.67	24	27	33	9	13	33	1	4	0	4	0	9
+22	9	5	33	190	21.11	13	21	33	20	5	33	1	4	0	3	1	9
+23	9	5	33	205	22.78	16	26	33	17	5	33	4	4	1	0	0	9
+24	9	5	33	247	27.44	28	31	33	5	21	33	1	5	1	2	0	9
+25	9	11	34	241	26.78	24	33	33	9	11	34	3	4	0	2	0	9
+26	9	5	33	212	23.56	18	31	33	15	5	33	0	6	0	3	0	9
+27	9	5	33	227	25.22	21	26	33	12	5	33	3	4	1	1	0	9
+28	9	21	33	255	28.33	24	31	33	9	21	33	2	4	3	0	0	9
+29	9	5	33	228	25.33	21	30	33	12	5	33	2	4	1	2	0	9
+30	9	10	33	213	23.67	16	28	33	17	10	33	3	4	2	0	0	9
+31	9	5	33	236	26.22	21	31	33	12	5	33	1	4	1	3	0	9
+32	9	5	33	210	23.33	12	29	33	21	5	33	3	3	0	3	0	9
+33	9	5	33	183	20.33	9	21	33	24	5	33	1	4	2	2	0	9
+34	9	5	33	150	16.67	7	17	22	15	5	33	3	4	1	1	0	9
+35	9	13	33	217	24.11	21	24	29	8	13	33	1	4	1	3	0	9
+36	9	5	33	195	21.67	18	21	32	14	5	33	3	2	1	3	0	9
diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-out1.png b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-out1.png
new file mode 100644
index 00000000000..aeac7234748
Binary files /dev/null and b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastx_nucleotides_distribution-out1.png differ
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml
new file mode 100644
index 00000000000..3113224771e
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fastq Manipulation
+- Statistics
+description: Compute quality statistics
+long_description: |
+  Creates quality statistics report for the given FASTQ library.
+name: fastx_quality_statistics
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml
new file mode 100644
index 00000000000..04465918747
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml
@@ -0,0 +1,72 @@
+<tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_quality_stats
+-o '$output'
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastq_input" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
+            <output name="output" file="fastq_stats1.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Creates quality statistics report for the given Solexa/FASTQ library.
+
+.. class:: infomark
+
+**TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
+
+-----
+
+**The output file will contain the following fields:**
+
+* column    = column number (1 to 36 for a 36-cycles read Solexa file)
+* count   = number of bases found in this column.
+* min     = Lowest quality score value found in this column.
+* max     = Highest quality score value found in this column.
+* sum     = Sum of quality score values for this column.
+* mean    = Mean quality score value for this column.
+* Q1    = 1st quartile quality score.
+* med    = Median quality score.
+* Q3    = 3rd quartile quality score.
+* IQR    = Inter-Quartile range (Q3-Q1).
+* lW    = 'Left-Whisker' value (for boxplotting).
+* rW    = 'Right-Whisker' value (for boxplotting).
+* A_Count    = Count of 'A' nucleotides found in this column.
+* C_Count    = Count of 'C' nucleotides found in this column.
+* G_Count    = Count of 'G' nucleotides found in this column.
+* T_Count    = Count of 'T' nucleotides found in this column.
+* N_Count = Count of 'N' nucleotides found in this column.
+
+For example::
+
+     1  6362991 -4 40 250734117 39.41 40 40 40  0 40 40 1396976 1329101  678730 2958184   0
+     2  6362991 -5 40 250531036 39.37 40 40 40  0 40 40 1786786 1055766 1738025 1782414   0
+     3  6362991 -5 40 248722469 39.09 40 40 40  0 40 40 2296384  984875 1443989 1637743   0
+     4  6362991 -4 40 248214827 39.01 40 40 40  0 40 40 2536861 1167423 1248968 1409739   0
+    36  6362991 -5 40 117158566 18.41  7 15 30 23 -5 40 4074444 1402980   63287  822035 245
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq
new file mode 100644
index 00000000000..d1bc160aa5d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+BBC?7?B6>ABB?B;BBBCC9&;BCBBBBBBBB>>A
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+8BBB?B;BB8?6@9B8BB=8.&1?,&;931&&&(BB
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+B@.?B=6BBB@.@BBBBBBBBBBBBBBB7=;6(663
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+B?BBBBBBBBBBBBBBB@6ABBBBB@4@BBBBB77<
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+CBCBBBBBBB6.BBBBBBBBBBB=9&66&1@>6&3&
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+B==2777-BB-0&96866&,66-&.6&66,6-*2.6
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+BBBBBBBBB9699&9BBBBBA@;BBBBBBBBB9&96
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+BB<4?A9ABB@>>009.6?@<.6@BBBBBBBBBBBB
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+BBBBBBBB?BBBBBBCCC<,91&6<39;?+6,3,9&
diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out
new file mode 100644
index 00000000000..852c8122efe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/test-data/fastq_stats1.out
@@ -0,0 +1,37 @@
+column	count	min	max	sum	mean	Q1	med	Q3	IQR	lW	rW	A_Count	C_Count	G_Count	T_Count	N_Count	Max_count
+1	9	23	34	288	32.00	33	33	33	0	33	33	3	1	4	1	0	9
+2	9	28	33	287	31.89	31	33	33	2	28	33	3	3	2	1	0	9
+3	9	13	34	268	29.78	28	33	33	5	21	34	5	1	0	3	0	9
+4	9	17	33	261	29.00	30	33	33	3	26	33	1	2	3	3	0	9
+5	9	22	33	269	29.89	30	33	33	3	26	33	3	3	3	0	0	9
+6	9	22	33	277	30.78	30	33	33	3	26	33	5	3	0	1	0	9
+7	9	21	33	258	28.67	24	33	33	9	21	33	4	1	3	1	0	9
+8	9	12	33	263	29.22	32	33	33	1	31	33	2	1	1	5	0	9
+9	9	29	33	290	32.22	33	33	33	0	33	33	3	3	2	1	0	9
+10	9	23	33	277	30.78	32	33	33	1	31	33	1	4	2	2	0	9
+11	9	12	33	245	27.22	21	31	33	12	12	33	5	2	1	1	0	9
+12	9	13	33	214	23.78	15	24	33	18	13	33	2	4	2	1	0	9
+13	9	5	33	249	27.67	29	31	33	4	23	33	2	1	1	5	0	9
+14	9	5	33	233	25.89	24	33	33	9	11	33	3	3	2	1	0	9
+15	9	15	33	251	27.89	24	33	33	9	15	33	5	1	1	2	0	9
+16	9	23	34	269	29.89	24	33	33	9	23	34	3	1	2	3	0	9
+17	9	13	34	266	29.56	33	33	33	0	33	33	2	3	1	3	0	9
+18	9	21	34	272	30.22	31	33	33	2	28	34	0	5	1	3	0	9
+19	9	5	34	244	27.11	27	30	33	6	18	34	4	4	1	0	0	9
+20	9	11	34	241	26.78	23	32	33	10	11	34	3	4	2	0	0	9
+21	9	13	33	240	26.67	24	27	33	9	13	33	1	4	0	4	0	9
+22	9	5	33	190	21.11	13	21	33	20	5	33	1	4	0	3	1	9
+23	9	5	33	205	22.78	16	26	33	17	5	33	4	4	1	0	0	9
+24	9	5	33	247	27.44	28	31	33	5	21	33	1	5	1	2	0	9
+25	9	11	34	241	26.78	24	33	33	9	11	34	3	4	0	2	0	9
+26	9	5	33	212	23.56	18	31	33	15	5	33	0	6	0	3	0	9
+27	9	5	33	227	25.22	21	26	33	12	5	33	3	4	1	1	0	9
+28	9	21	33	255	28.33	24	31	33	9	21	33	2	4	3	0	0	9
+29	9	5	33	228	25.33	21	30	33	12	5	33	2	4	1	2	0	9
+30	9	10	33	213	23.67	16	28	33	17	10	33	3	4	2	0	0	9
+31	9	5	33	236	26.22	21	31	33	12	5	33	1	4	1	3	0	9
+32	9	5	33	210	23.33	12	29	33	21	5	33	3	3	0	3	0	9
+33	9	5	33	183	20.33	9	21	33	24	5	33	1	4	2	2	0	9
+34	9	5	33	150	16.67	7	17	22	15	5	33	3	4	1	1	0	9
+35	9	13	33	217	24.11	21	24	29	8	13	33	1	4	1	3	0	9
+36	9	5	33	195	21.67	18	21	32	14	5	33	3	2	1	3	0	9
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml
new file mode 100644
index 00000000000..7ccac40405c
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Fastq Manipulation
+description: Rename sequences
+long_description: |
+  This tool renames the sequence identifiers in a FASTQ/A file.
+name: fastx_renamer
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml
new file mode 100644
index 00000000000..44a3b2030b2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml
@@ -0,0 +1,75 @@
+<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_renamer
+-n $TYPE
+-o '$output'
+-v
+@FQQUAL@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastx_input" />
+
+        <param name="TYPE" type="select" label="Rename sequence identifiers to">
+            <option value="SEQ">Nucleotides sequence</option>
+            <option value="COUNT">Numeric Counter</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastx_renamer-in1.fastq" />
+            <param name="TYPE" value="SEQ" />
+            <output name="output" file="fastx_renamer-out1.fastq" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool renames the sequence identifiers in a FASTQ/A file.
+
+.. class:: infomark
+
+Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
+
+--------
+
+**Example**
+
+The following Solexa-FASTQ file::
+
+    @CSHL_4_FC042GAMMII_2_1_517_596
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    +CSHL_4_FC042GAMMII_2_1_517_596
+    40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+
+Renamed to **nucleotides sequence**::
+
+    @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+
+Renamed to **numeric counter**::
+
+    @1
+    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+    +1
+    40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/macros.xml b/tool_collections/fastx_toolkit/fastx_renamer/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq
new file mode 100644
index 00000000000..d3386dda038
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-in1.fastq
@@ -0,0 +1,36 @@
+@CSHL_3_FC042AGLLWW:1:2:7:203
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++CSHL_3_FC042AGLLWW:1:2:7:203
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CSHL_3_FC042AGLLWW:1:2:7:33
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CSHL_3_FC042AGLLWW:1:2:7:33
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@CSHL_3_FC042AGLLWW:1:2:7:169
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:169
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@CSHL_3_FC042AGLLWW:1:2:7:1436
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++CSHL_3_FC042AGLLWW:1:2:7:1436
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@CSHL_3_FC042AGLLWW:1:2:7:292
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++CSHL_3_FC042AGLLWW:1:2:7:292
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@CSHL_3_FC042AGLLWW:1:2:7:1819
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++CSHL_3_FC042AGLLWW:1:2:7:1819
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@CSHL_3_FC042AGLLWW:1:2:7:1875
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++CSHL_3_FC042AGLLWW:1:2:7:1875
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@CSHL_3_FC042AGLLWW:1:2:8:624
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++CSHL_3_FC042AGLLWW:1:2:8:624
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@CSHL_3_FC042AGLLWW:1:2:8:250
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++CSHL_3_FC042AGLLWW:1:2:8:250
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq
new file mode 100644
index 00000000000..80c7c79e4c0
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/fastx_renamer-out1.fastq
@@ -0,0 +1,36 @@
+@GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
++GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT
+aab^V^aU]`aa^aZaaabbXEZabaaaaaaaa]]`
+@CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
++CAATGCCTCCAATTGGTTAATCCCCCTATATATACT
+Waaa^aZaaW^U_XaWaa\WMEP^KEZXRPEEEGaa
+@GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
++GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC
+a_M^a\Uaaa_M_aaaaaaaaaaaaaaaV\ZUGUUR
+@AATTATTTATTAAATTTTAATAATATGGGAGACACT
+AATTATTTATTAAATTTTAATAATATGGGAGACACT
++AATTATTTATTAAATTTTAATAATATGGGAGACACT
+a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[
+@GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+GGAGAAATACACACAATTGGTTAATCCCCCTATATA
++GGAGAAATACACACAATTGGTTAATCCCCCTATATA
+babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE
+@AATTCAAACCACCCCAACCCACACACAGAGATACAA
+AATTCAAACCACCCCAACCCACACACAGAGATACAA
++AATTCAAACCACCCCAACCCACACACAGAGATACAA
+a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU
+@GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
++GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC
+aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU
+@ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
++ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG
+aa[S^`X`aa_]]OOXMU^_[MU_aaaaaaaaaaaa
+@TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
+TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
++TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA
+aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa
new file mode 100644
index 00000000000..6dd52e0c643
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa
@@ -0,0 +1,4 @@
+@CSHL_4_FC042GAMMII_2_1_517_596
+GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
++CSHL_4_FC042GAMMII_2_1_517_596
+40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa
new file mode 100644
index 00000000000..2dfe3ffbe82
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa
@@ -0,0 +1,4 @@
+@GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
++GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
+40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml
new file mode 100644
index 00000000000..6a9dcbb313d
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/.shed.yml
@@ -0,0 +1,12 @@
+categories:
+- Fastq Manipulation
+- Fasta Manipulation
+description: Reverse-Complement
+long_description: |
+  This tool reverse-complements each sequence in a library. If the
+  library is a FASTQ, the quality-scores are also reversed.
+name: fastx_reverse_complement
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml
new file mode 100644
index 00000000000..547b0c4d99a
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml
@@ -0,0 +1,62 @@
+<tool id="cshl_fastx_reverse_complement" version="1.0.1" name="Reverse-Complement">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_reverse_complement -v
+-o '$output'
+@FQQUAL@
+    ]]></command>
+    <inputs>
+        <expand macro="fastx_input" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Reverse-complement a FASTA file -->
+            <param name="input" value="fastx_rev_comp1.fasta" />
+            <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" />
+        </test>
+        <test>
+            <!-- Reverse-complement a FASTQ file -->
+            <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
+            <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool reverse-complements each sequence in a library.
+If the library is a FASTQ, the quality-scores are also reversed.
+
+--------
+
+**Example**
+
+Input FASTQ file::
+
+    @CSHL_1_FC42AGWWWXX:8:1:3:740
+    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
+    +CSHL_1_FC42AGWWWXX:8:1:3:740
+    33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
+
+
+Output FASTQ file::
+
+    @CSHL_1_FC42AGWWWXX:8:1:3:740
+    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
+    +CSHL_1_FC42AGWWWXX:8:1:3:740
+    26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta
new file mode 100644
index 00000000000..6767ab70655
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp1.fasta
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq
new file mode 100644
index 00000000000..c9bb2c58d03
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_rev_comp2.fastq
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
++CSHL__2_FC042NGABCD:8:1:120:202
+40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
++CSHL__2_FC042NGABCD:8:1:103:1185
+40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out
new file mode 100644
index 00000000000..0707c85dc3f
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement1.out
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT
+>CSHL__2_FC042NGABCD:8:1:103:1185
+GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT
diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out
new file mode 100644
index 00000000000..65997ea46c2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/test-data/fastx_reverse_complement2.out
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+GCAGAAAACGGCATACTAGCTCTTCCGATCTATCGT
++CSHL__2_FC042NGABCD:8:1:120:202
+8 10 21 -1 10 11 -1 7 3 1 8 40 27 14 40 30 -1 40 20 40 25 40 40 28 40 40 6 40 40 40 40 20 40 40 40 40
+@CSHL__2_FC042NGABCD:8:1:103:1185
+GAAGACGGTAAACGAGCTCTGCCGATCTATCGTGAT
++CSHL__2_FC042NGABCD:8:1:103:1185
+2 30 25 4 2 8 0 10 3 23 12 22 34 15 36 8 14 17 22 9 0 40 22 30 32 40 40 40 31 33 35 40 40 40 40 40
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml
new file mode 100644
index 00000000000..461bf74566c
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/.shed.yml
@@ -0,0 +1,11 @@
+categories:
+- Fasta Manipulation
+- Fastq Manipulation
+description: Trim sequences
+long_description: |
+  This tool trims (cut bases from) sequences in a FASTA/Q file.
+name: fastx_trimmer
+owner: devteam
+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer
+type: unrestricted
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml
new file mode 100644
index 00000000000..c6d2341f9a4
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml
@@ -0,0 +1,76 @@
+<tool id="cshl_fastx_trimmer" version="1.0.1" name="Trim sequences">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_trimmer -v
+-f $first
+-l $last
+-o '$output'
+@FQQUAL@
+    ]]></command>
+    <inputs>
+        <expand macro="fastx_input" />
+        <param name="first" type="integer" value="1" label="First base to keep" />
+        <param name="last" type="integer" value="21" label="Last base to keep" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
+            <param name="input" value="fastx_trimmer1.fasta" />
+            <param name="first" value="5"/>
+            <param name="last" value="36"/>
+            <output name="output" ftype="fasta" file="fastx_trimmer1.out" />
+        </test>
+        <test>
+            <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
+            <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
+            <param name="first" value="1"/>
+            <param name="last" value="27"/>
+            <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool trims (cut bases from) sequences in a FASTA/Q file.
+
+--------
+
+**Example**
+
+Input Fasta file (with 36 bases in each sequences)::
+
+    >1-1
+    TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
+    >2-1
+    CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
+
+Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
+
+    >1-1
+    TATGGTCAGAAACCATATGCA
+    >2-1
+    CAGCGAGGCTTTAATGCCATT
+
+Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
+
+    >1-1
+    TCAGA
+    >2-1
+    AGGCT
+
+    ------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+    ]]></help>
+    <expand macro="citations" />
+<!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+</tool>
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml b/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml
new file mode 120000
index 00000000000..0c6ff6c3756
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/macros.xml
@@ -0,0 +1 @@
+../macros.xml
\ No newline at end of file
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta
new file mode 100644
index 00000000000..6767ab70655
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.fasta
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out
new file mode 100644
index 00000000000..94f4a66b037
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer1.out
@@ -0,0 +1,4 @@
+>CSHL__2_FC042NGABCD:8:1:120:202
+TAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
+>CSHL__2_FC042NGABCD:8:1:103:1185
+CGATAGATCGGCAGAGCTCGTTTACCGTCTTC
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq
new file mode 100644
index 00000000000..c9bb2c58d03
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.fastq
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
++CSHL__2_FC042NGABCD:8:1:120:202
+40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
++CSHL__2_FC042NGABCD:8:1:103:1185
+40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out
new file mode 100644
index 00000000000..bf2127ccfbe
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_trimmer/test-data/fastx_trimmer2.out
@@ -0,0 +1,8 @@
+@CSHL__2_FC042NGABCD:8:1:120:202
+ACGATAGATCGGAAGAGCTAGTATGCC
++CSHL__2_FC042NGABCD:8:1:120:202
+40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1
+@CSHL__2_FC042NGABCD:8:1:103:1185
+ATCACGATAGATCGGCAGAGCTCGTTT
++CSHL__2_FC042NGABCD:8:1:103:1185
+40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 0 9 22 17 14 8 36 15 34 22 12 23
diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml
new file mode 100644
index 00000000000..8e70d9b99d2
--- /dev/null
+++ b/tool_collections/fastx_toolkit/macros.xml
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@CATS@">
+        #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+            zcat -f '$input' |
+        #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+            bzcat -f '$input' |
+        #else:
+            cat '$input' |
+        #end if
+    </token>
+    <token name="@FQQUAL@">
+        <![CDATA[
+            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
+                -Q 33
+            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
+                -Q 64
+            #end if
+        ]]>
+    </token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@VERSION@">0.0.14</token>
+    <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
+    <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
+    <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
+    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
+    <token name="@FASTAS@">fasta,fasta.gz</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{agordon,
+                    author = "Assaf Gordon",
+                    title = "FASTQ/A short-reads pre-processing tools",
+                    year = "2010",
+                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
+                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="fasta_input">
+        <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
+    </xml>
+    <xml name="fastq_input">
+        <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
+    </xml>
+    <xml name="fastx_input">
+        <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
+    </xml>
+</macros>