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wgsim(1) Bioinformatics tools wgsim(1) NAME wgsim - Whole-genome sequencing read simulator SYNOPSIS 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. 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-1.23.1 18 March 2026 wgsim(1)
NAME | SYNOPSIS | OPTIONS | AUTHOR
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