Alternatives to Transrate

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3.7 years ago

Dunois ★ 2.5k

Transrate is basically dead (the dev confirmed as much in its Gitter chat recently; rest in peace), and the last version out (v1.0.3) is known to be buggy (see Low transrate assembly score with good bowtie2 mapping? and the numerous issues on its GitHub page). This means that one of the most used transcriptome assembly evaluation tools is no longer really usable.

My question is: are there any modern alternatives to Transrate as of 2020? I've been searching online, but in vain. I'm hoping perhaps somebody else has come across something.

Assembly RNA-Seq quality control evaluation • 1.0k views

ADD COMMENT • link updated 3.7 years ago by Biostar 20 • written 3.7 years ago by Dunois ★ 2.5k

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rnaQuast: http://cab.spbu.ru/software/rnaquast/
You could also try BUSCO to see how complete your assembly is.

ADD REPLY • link 3.7 years ago by GenoMax 142k

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@genomax, I'll give rnaQuast a try. BUSCO isn't really quite equivalent to Transrate though, is it?

ADD REPLY • link 3.7 years ago by Dunois ★ 2.5k

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