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Read Generator With Clear Annotation Of Read Origin And Mutations

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!

short next-gen sequencing simulation alignment
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Travis Travis

2 answers

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

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written by Jts • Jts

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

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written by Travis Travis

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.

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written by Jts • Jts

The samtools package contains a utility named wgsim

Program: wgsim (short read simulator)
Version: 0.2.3
Contact: Heng Li <lh3@sanger.ac.uk>

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

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Travis Travis

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

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written by Travis Travis

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