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How To Generate Synthetic Read Data From An Existing Fasta

I have several draft genome assemblies that are in fasta format.

I would like to create synthetic read data from these fastas- basically break the fastas up into overlapping fragments of 100bp or so and simulate an SRA.

Is there already a tool available that can do this?

fasta sequence reads
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updated by Ram Ram • written by smith.tracymae • smith.tracymae

1 answer

There are a large number of options out there. wgsim was written by Heng Li and has been pretty heavily used. I've been using Sherman a lot recently, mostly because it can also simulate MethylC-seq reads. Just to list a few more: ART, SimSeq and Flux Simulator. I'll add, search for "short read simulator" or something along those lines for even more options.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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