wgsim(1) Bioinformatics tools wgsim(1)NAMEwgsim - Whole-genome sequencing read simulator
SYNOPSISwgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>
<in.ref.fa> must be a fasta file containing a reference genome.
<out.read1.fq> and <out.read2.fq> are the first and second read output
files.
OPTIONS-e FLOAT
base error rate [0.000]
-d INT outer distance between the two ends [500]
-s INT standard deviation [50]
-N INT number of read pairs [1000000]
-1 INT length of the first read [70]
-2 INT length of the second read [70]
-r FLOAT
rate of mutations [0.0010]
-R FLOAT
fraction of indels [0.15]
-X FLOAT
probability an indel is extended [0.30]
-S INT seed for random generator [-1]
-A FLOAT
discard if the fraction of ambiguous bases higher than FLOAT
[0.05]
-h haplotype mode
Parameter defaults are given in square brackets.
AUTHOR
Copyright 2008 Genome Research Limited.
Copyright 2011 Heng Li.
wgsim is part of samtools, https://github.com/samtools/samtools
samtools-1.3 15 December 2015 wgsim(1)