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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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Don't use map quality filtering in binning #650

Closed johnne closed 1 year ago

johnne commented 1 year ago

Since the vamb developers stress that map quality should not be used to filter bam files for binning I removed the minmapq param from pileup.sh in the binning rulesfile. As far as I can tell the coverage from pileup in that part of atlas is passed only to MaxBin2 and CONCOCT, which means that neither vamb nor Metabat2 are affected anway (as these use bam files directly, or depth values calculated in other ways from bam files).

SilasK commented 1 year ago

Thank you for digging into this.

The vamb and semibin workflows are separated from the other binners because they use the cobining workflow.

do you think we can keep the minimap quality for metabat and don't have it for vamb and semibin?

johnne commented 1 year ago

I tried to find mention of map quality in Metabat2 and Maxbin2 sources but didn't come across anything. Also spoke with the developer of concoct but nothing there related to mapq either. Feels like it's either overlooked or not a big issue, so I guess it's probably no harm to keep it in.