updated pre-built models and modif doc accordingly

README.md

@@ -37,16 +37,17 @@ cases.
 
 ### Generate reads with a pre-computed error model
 
-for generating 1M reads using the HiSeq 2500 error model:
+for generating 1M reads using the MiSeq300bp error model:
 
 ```shell
 iss generate --genomes genomes.fasta --abundance abundance_file.txt \
-    --model_file HiSeq2500 --output HiSeq_reads
+    --model_file MiSeq300bp --output HiSeq_reads
 ```
 
 where `genomes.fasta` is a (multi-)fasta file containing the reference genome from which the simulated reads will be generated, and `abundance_file.txt` a tab-delimited file containing abundance information.
 
-Currently InSilicoSeq comes with 2 error models: `HiSeq2500` and `MiSeq`
+Currently InSilicoSeq comes with 3 error models: `HiSeq2500`, `MiSeq250bp` and
+`MiSeq300bp`
 
 ### Example of genomes and abundance file
 
@@ -72,16 +73,16 @@ InSilicoSeq, it is possible to create your own.
 Align you reads against the reference:
 
 ```shell
-    bowtie2-build genome.fasta genome
-    bowtie2 -x genome -1 reads_R1.fastq.gz \
-        -2 reads_R2.fastq.gz | samtools view -bS | samtools sort -o genome.bam
-    samtools index genome.bam
+    bowtie2-build genomes.fasta genomes
+    bowtie2 -x genomes -1 reads_R1.fastq.gz \
+        -2 reads_R2.fastq.gz | samtools view -bS | samtools sort -o genomes.bam
+    samtools index genomes.bam
 ```
 
 then build the model:
 
 ```shell
-    iss model -b genome.bam -o genome
+    iss model -b genomes.bam -o genomes
 ```
 
 which will create a `genome.npz` file containing your newly built model

doc/iss/generate.rst

@@ -10,13 +10,13 @@ to easily generate reads from:
 - MiSeq (250bp)
 - MiSeq (300bp)
 
-Per example generate 1 million HiSeq 2500 reads from a set of input genomes
+Per example generate 1 million MiSeq 300bp reads from a set of input genomes
 with an abundance file:
 
 .. code-block:: bash
 
     iss generate --genomes genomes.fasta --abundance abundance_file.txt \
-        --model_file HiSeq2500 --output HiSeq_reads
+        --model_file MiSeq300bp --output MiSeq_reads
 
 
 If you have created your custom model, just give the .npz file to --model_file

doc/iss/model.rst

@@ -16,15 +16,15 @@ Align you reads against the reference:
 
 .. code-block:: bash
 
-    bowtie2-build genome.fasta genome
-    bowtie2 -x genome -1 reads_R1.fastq.gz \
-        -2 reads_R2.fastq.gz | samtools view -bS | samtools sort -o genome.bam
-    samtools index genome.bam
+    bowtie2-build genomes.fasta genomes
+    bowtie2 -x genomes -1 reads_R1.fastq.gz \
+        -2 reads_R2.fastq.gz | samtools view -bS | samtools sort -o genomes.bam
+    samtools index genomes.bam
 
 then build the model:
 
 .. code-block:: bash
 
-    iss model -b genome.bam -o genome
+    iss model -b genomes.bam -o genomes
 
-which will create a `genome.npz` file containing your newly built model
+which will create a `genomes.npz` file containing your newly built model