Generating synthetic TB reads

Question

[matt81rd]

Hi All,

I was wondering if anyone has any knowledge on tools for generating synthetic reads. I will specifically be using it to generate synthetic TB reads but any knowledge is greatly appreciated. I need these reads to test a tool that's being developed. I was made aware of ART but was wondering if a new more reliable tool has come out in recent years? Any info would be appreciated!

Cheers

[GenoMax]

What does TB reads stand for? Reads for Mycobacterium tuberculosis or is that an acronym that is non-standard? If latter please provide full form.

Answer 1

[harold.smith.tarheel]

You can use the randomreads function of BBMap; tutorial posted in this thread.

Answer 2

[Mensur Dlakic]

I don't think you need anything better or more reliable than ART, except maybe for the most recent long sequencing technologies.

wgsim is and oldie but goodie.

https://github.com/lh3/wgsim

To drive both programs:

https://github.com/wanyuac/readSimulator

Answer 3

[colindaven]

For completeness, badread by rrwick is good for nanopore reads.

https://github.com/rrwick/Badread