update iss generate doc

doc/iss/generate.rst

@@ -3,10 +3,19 @@
 Generating reads
 ================
 
+InSilicoSeq can simulate amplicon reads, or reads from whole metagenome sequencing (the default).
+You can specify the type of reads you want to simulate with the ``--sequence_type`` option.
+
 InSilicoSeq comes with a set of pre-computed error models to allow the user to easily generate reads from the most popular Illumina instruments:
 
 - HiSeq
-- MiSeq
+- MiSeq (optionally, with various quality thresholds):
+    - MiSeq-20
+    - MiSeq-24
+    - MiSeq-28
+    - MiSeq-32
+    - MiSeq-36
+- NextSeq
 - NovaSeq
 
 Per example generate 1 million MiSeq reads from a set of input genomes:
@@ -49,6 +58,19 @@ You can also provide multiple input files:
     curl -O -J -L https://osf.io/37kg8/download  # download another example file
     iss generate --genomes SRS121011.fasta minigut.fasta --n_genomes 5 --model novaseq --output novaseq_reads
 
+Amplicons
+---------
+
+To generate amplicon reads, use the ``--sequence_type amplicon`` option:
+
+.. code-block:: bash
+
+    # no example data is provided here
+    iss generate --genomes my_amplicons.fasta ---readcount_file counts.txt -sequence_type amplicon --model nextseq --output reads
+
+where ``counts.txt`` is a tab-delimited file containing the number of reads to generate for each amplicon sequence present in ``my_amplicons.fasta``.
+Alternatively, you can use the ``--n_reads`` option to generate a fixed number of reads, together with an abundance distribution.
+
 Draft genomes
 -------------
 
@@ -230,6 +252,11 @@ coverage distribution. Can be uniform, halfnormal, exponential, lognormal or zer
 
 file containing coverage information (default: None).
 
+--readcount_file
+^^^^^^^^^^^^^^^^
+
+file containing read_count information (default: None).
+
 --n_reads
 ^^^^^^^^^
 
@@ -246,16 +273,21 @@ Can be 'kde' or 'basic'
 ^^^^^^^^
 
 Error model file. (default: None).
-Use HiSeq, NovaSeq or MiSeq for a pre-computed error model provided with the software, or a file generated with iss model.
-If you do not wish to use a model, use --mode basic.
-The name of the built-in models is case insensitive.
+Use HiSeq, NextSeq, NovaSeq, MiSeq or Miseq-[20,24,28,32] for a pre-computed error model provided with the software, or a file generated with iss model.
+If you do not wish to use a model, use --mode basic or --mode perfect.
+The name of the built-in models are case insensitive.
 
 --gc_bias
 ^^^^^^^^^
 
 If set, may fail to sequence reads with abnormal GC content.
 Does not guarantee --n_reads (default: False)
 
+--sequence_type
+^^^^^^^^^^^^^^^
+
+Type of sequencing. Can be metagenomics or amplicon (default: metagenomics).
+
 --cpus
 ^^^^^^
 
@@ -284,4 +316,9 @@ Output file path and prefix (Required)
 --compress
 ^^^^^^^^^^
 
-Compress the output in gzip format (default: False).
+Compress the output in gzip format (default: False).
+
+--store_mutations
+^^^^^^^^^^^^^^^^^
+
+Generates an additional VCF file with the mutations introduced in the reads (bool).

iss/app.py

@@ -344,9 +344,9 @@ def main():
         "-m",
         metavar="<npz>",
         default=None,
-        help="Error model file. (default: %(default)s). Use HiSeq, NovaSeq or \
-        MiSeq for a pre-computed error model provided with the software, or a \
-        file generated with iss model. If you do not wish to use a model, use \
+        help="Error model file. (default: %(default)s). Use HiSeq, NextSeq, NovaSeq, \
+        MiSeq or Miseq-[20,24,28,32] for a pre-computed error model provided with the \
+        software, or a file generated with iss model. If you do not wish to use a model, use \
         --mode basic or --mode perfect. The name of the built-in models are  \
         case insensitive.",
     )