Question: Read Generator With Clear Annotation Of Read Origin And Mutations
2
gravatar for Travis
7.6 years ago by
Travis2.8k
USA
Travis2.8k wrote:

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!

ADD COMMENTlink modified 7.0 years ago by Pierre Lindenbaum118k • written 7.6 years ago by Travis2.8k
2
gravatar for Jts
7.6 years ago by
Jts1.2k
Jts1.2k wrote:

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

ADD COMMENTlink written 7.6 years ago by Jts1.2k
2

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.

ADD REPLYlink written 7.6 years ago by Jts1.2k

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

ADD REPLYlink written 7.6 years ago by Travis2.8k
1
gravatar for Pierre Lindenbaum
7.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

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.

ADD COMMENTlink written 7.6 years ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 7.6 years ago by Travis2.8k

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

ADD REPLYlink written 7.6 years ago by Travis2.8k
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