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Russel88 / MAGinator

MAGinator - Accurate SNV calling and profiling of MAGs
MIT License
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Is it working with Viruses? #8

Open rdenise opened 1 year ago

rdenise commented 1 year ago

Hello,

I was wondering is it possible to have it work working with viruses to create vMAGs?

Best,

Russel88 commented 1 year ago

In principle it could work with viruses. If you use VAMB to bin, it will also bin viruses. By default all bins below the size of 200kb are removed, but that cutoff could be lowered to include viruses. However, currently it is hardcoded that each species should have 100 signature genes, which is very unlikely to find for viruses, but we could make an option to change this.

rdenise commented 11 months ago

Also I don't know if GTDB-tk is suitable for viruses. But maybe I am wrong

Russel88 commented 10 months ago

No GTDB-tk does not annotate viruses (or eukaryotes), but maginator still profiles with clusters of bins that are unannotated