Question: Overlapping paired end read simulator
gravatar for eheizer31
4.0 years ago by
United States
eheizer310 wrote:

I am trying to create some synthetic datasets.  The reads in the datasets need to be 150bp and paired end.  I want the read pairs to overlap to some extent.  I have been using MetaSim but it does not seem to be able to make overlapping reads.  Does anyone have any suggestions?  NeSSM appears to allow for a gap but not an overlap.

ADD COMMENTlink modified 4.0 years ago by Brian Bushnell17k • written 4.0 years ago by eheizer310
gravatar for Brian Bushnell
4.0 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

BBMap's RandomReads tool [] will do that. For example: ref=ecoli.fasta out=synth.fq.gz paired interleaved reads=100k length=150 mininsert=200 maxinsert=400 adderrors gaussian

That will result in insert sizes from 200bp to 400bp, with a Gaussian distribution, so about 50% of the reads will overlap.

ADD COMMENTlink modified 1 day ago by RamRS25k • written 4.0 years ago by Brian Bushnell17k
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