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WGSIM(1) User Commands WGSIM(1)


wgsim - short read simulator


wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>


base error rate [0.020]
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]
haplotype mode


The software was written by Heng Li <>

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

December 2015 wgsim 1.2