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wgsim(1) Bioinformatics tools wgsim(1)

wgsim - Whole-genome sequencing read simulator

wgsim [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.

-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.

Copyright 2008 Genome Research Limited.
Copyright 2011 Heng Li.
wgsim is part of samtools, https://github.com/samtools/samtools
21 February 2022 samtools-1.15

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