Can BBTools Dedupe be used in transcriptome assembly clustering ?

Question

[VineethVenumadhavan]

Dear Team, Curious to know if dedup(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/dedupe-guide/) can be used for clustering transcriptome assemblies. I have to cluster my assembly with n% identity. When used dedup as follows dedupe.sh in=assembly.fa out=Clustered_Assembly.fa -Xmx100g minidentity=n threads=40, we got the results lightning fast with compared to cd-hit-est. Please comment

Answer 1

[GenoMax]

While there is no specific reason why it can't be used (after all it is only looking at sequence) you should look through the before and after results to make sure they look reasonable.

You may also want to look at the concept of super transcripts (see: A: merge trinscripts id from results trinity ) if aim is to collapse isoforms into one representation.

[VineethVenumadhavan]

This certainly is helping me :)