Read Generator With Clear Annotation Of Read Origin And Mutations

Question

[Travis]

Hi all,

Does an NGS read simulator exist that will output reads along with their chromosome/coordinates of origin, position and type of mutation/error introduced etc?

I want to assess some aligners and the better annotated the reads in terms of their composition, the better!

Answer 1

[Jts]

John St John's SimSeq program outputs the sampled reads as a SAM file, which would provide you with the position and orientation. I don't think it tracks the position of introduced errors but it would not be too difficult to change the code to write this information as an MD tag.

https://github.com/jstjohn/SimSeq

[Jts]

Well, if such software doesn't exist SimSeq would be a good place to start. Alternatively, you could run samtools calmd on the SimSeq output with the original reference to fill in the MD tag.

[Travis]

My real motive here is to find out whether software exists to perform the task at hand without alteration/rewriting.

Answer 2

[Pierre Lindenbaum]

The samtools package contains a utility named wgsim

Program: wgsim (short read simulator)
Version: 0.2.3
Contact: Heng Li <[e-mail]>

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

It generates some short reads and a pileup file containing the mutations.

[Travis]

Although it does not appear to give the mapping location of the reads or associate the read with the mutations

[Travis]

Although it does not appear to associate the read with the mutations