wgsim

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-1.9                      18 July 2018                          wgsim(1)