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simulate reads with zero mutations

Hi,

I'm interested in simulating reads with a mutation rate of zero. So basically I just want to generate reads of a certain length without any mutations. Is there a way to do this with wgsim or perhaps Art? Thanks!

wgsim
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updated by Ram Ram • written by jyu429 jyu429

1 answer 

$ wgsim

Program: wgsim (short read simulator)
Version: 0.3.0
Contact: Heng Li <lh3@sanger.ac.uk>

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

Options: -e FLOAT      base error rate [0.020]
         -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]
         -h            haplotype mode

->

wgsim -e 0.0 -r 0.0 <in.ref.fa> <out.read1.fq> <out.read2.fq>
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! Is there also a parameter to play with read-depth coverage?

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written by jyu429 jyu429

If you know the size of the genome, which you do, coverage is reads*readLength/geneomeLength, and the number of reads and their length are parameters.

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written by Brian Bushnell Brian Bushnell

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