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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Make eggnog mapper use mmseqs2? #74

Closed LeeBergstrand closed 10 months ago

LeeBergstrand commented 10 months ago

Problem Description

Eggnog mapper takes a long time to run.

Problem Solution

I was going through eggnog mapper's command line options. You have the option of running it with diamond, mmseqs2, or hammer. My understanding is that mmseqs2 is faster than diamond. I was wondering why the diamond option was chosen as the eggnog search tool? Was there sensitivity issues?

jmtsuji commented 10 months ago

@LeeBergstrand Just checked the eggnog-mapper article, and it appears that mmseqs2 is faster than DIAMOND with non-huge datasets and has comparable sensitivity to DIAMOND, based on their testing. Because we are using a genome annotation pipeline, let's use mmseqs!

LeeBergstrand commented 10 months ago

@jmtsuji Okay, I will address this.

LeeBergstrand commented 10 months ago

@jmtsuji Addressed in https://github.com/jmtsuji/rotary/pull/73/commits/dd96bbc1516b0c95d40068091c9173b702419e5b