recommend a short reads simulator?

[schönblick]

can any one recommend a short reads (illumina) simulator?

[jts]

I use SimSeq by John St. John:

https://github.com/jstjohn/SimSeq

[steven]

You may want to try the Flux Simulator too

[suryasaha]

Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.

Program: wgsim (short read simulator)
Version: 0.2.3
Contact: Heng Li <[email protected]>

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 [0.10]
         -X FLOAT      probability an indel is extended [0.30]
         -c            generate reads in color space (SOLiD reads)
         -C            show mismatch info in comment rather than read name
         -h            haplotype mode

Note: For SOLiD reads, the first read is F3 and the second is R3.

[schönblick]

thanks all for suggestions!

[mdk308]

Samtools includes the wgsim read simulator. It will be in the samtools-XXXX/misc/ directory after you install Samtools.

any idea how wgsim handles multifasta files? do i need to remove all of the headers or can i just run as is?

[lyz1030]

can anyone tell me how wgsim simulate variants (the position can be specified ) or we can get the variant position. The objective is to evaluate the false negative rate of variant calling softwares.