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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-1.10			6 December 2019			      wgsim(1)

NAME | SYNOPSIS | OPTIONS | AUTHOR

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