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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.


base error rate [0.000]
outer distance between the two ends [500]
standard deviation [50]
number of read pairs [1000000]
-1 INT
length of the first read [70]
-2 INT
length of the second read [70]
rate of mutations [0.0010]
fraction of indels [0.15]
probability an indel is extended [0.30]
seed for random generator [-1]
discard if the fraction of ambiguous bases higher than FLOAT [0.05]
haplotype mode


Copyright 2008 Genome Research Limited.
Copyright 2011 Heng Li.
12 December 2023 samtools-1.19