Overlapping paired end read simulator

Question

[eheizer31]

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.

Answer 1

[Brian Bushnell]

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.