wgsim man page on DragonFly

wgsim man page on DragonFly

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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-1.3		       15 December 2015			      wgsim(1)

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