Question

Generating synthetic TB reads

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2.1 years ago

matt81rd ▴ 10

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

Synthetic TB Sequences Genomic • 882 views

ADD COMMENT • link updated 2.1 years ago by GenoMax 147k • written 2.1 years ago by matt81rd ▴ 10

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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.

ADD REPLY • link 2.1 years ago by GenoMax 147k

score 2 · Answer 1 · 2022-10-12

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2.1 years ago

harold.smith.tarheel ★ 5.0k

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

ADD COMMENT • link 2.1 years ago by harold.smith.tarheel ★ 5.0k

score 2 · Answer 2 · 2022-10-12

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2.1 years ago

Mensur Dlakic ★ 28k

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

ADD COMMENT • link 2.1 years ago by Mensur Dlakic ★ 28k

score 2 · Answer 3 · 2022-10-12

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2.1 years ago

colindaven 7.0k

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

https://github.com/rrwick/Badread

ADD COMMENT • link 2.1 years ago by colindaven 7.0k