Any tools available to generate fake raw reads from assembled genomes?

Question

[Jenez]

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!

[GenoMax]

I second using randomreads.sh from BBMap but in case you want more options take a look at this thread: NGS reads simulation

[Jenez]

Oh shit I certainly did not google this well enough. Thanks!

Answer 1

[harold.smith.tarheel]

BBMap's 'randomreads' does exactly what you need.

[Jenez]

Thanks mate!. I need to better my search skills...

Answer 2

[ivivek_ngs]

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.

Answer 3

[Gabriel R.]

I have used ART http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ I have been satisfied with the results.