simulate reads with zero mutations

Question

[jyu429]

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!

Answer 1

[Pierre Lindenbaum]

$ wgsim

Program: wgsim (short read simulator)
Version: 0.3.0
Contact: Heng Li <[e-mail]>

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>

[jyu429]

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

[Brian Bushnell]

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.

[Pierre Lindenbaum]

see option '-N'