Hello fellow bioinformaticians!
I was wondering if anyone had any clue as to whether or not a tool exists for generating dummy/fake reads from an already assembled genome? So far my searches have yielded very little...
Essentially, the ideal software would take a single-contig assembled genome and generate simulated raw reads based on some input criteria such as desired average coverage, level of base quality, etc... .
People are not always nice enough to release the raw reads from their sequencing projects, hence simulated raw reads is the second best thing.
I realize this might be a very difficult task, but assuming no tool exists for this, do you think it would be possible to make a decent one?
Thank you for the input!
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written
by
Jenez
3 answers
BBMap's 'randomreads' does exactly what you need.
If you are in need for generating simulated RNA-Seq raw reads then you have polyester that should be able to do the trick for you.
I have used ART http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ I have been satisfied with the results.
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I second using
randomreads.shfrom BBMap but in case you want more options take a look at this thread: NGS reads simulationOh shit I certainly did not google this well enough. Thanks!