Question: How To Generate Synthetic Read Data From An Existing Fasta
0
gravatar for smith.tracymae
5.8 years ago by
smith.tracymae0 wrote:

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 reads tools sequence • 2.3k views
ADD COMMENTlink modified 5.8 years ago by Devon Ryan92k • written 5.8 years ago by smith.tracymae0
6
gravatar for Devon Ryan
5.8 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Devon Ryan92k
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