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.

-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.