Question: Overlapping paired end read simulator
0
gravatar for eheizer31
3.3 years ago by
eheizer310
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 3.3 years ago by Brian Bushnell16k • written 3.3 years ago by eheizer310
2
gravatar for Brian Bushnell
3.3 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

BBMap's RandomReads tool [randomreads.sh] will do that.  For example:

randomreads.sh 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 3.3 years ago • written 3.3 years ago by Brian Bushnell16k
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