How to know which viral sequences are not used in binning?

AnantharamanLab / vRhyme

Binning Virus Genomes from Metagenomes

GNU General Public License v3.0

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How to know which viral sequences are not used in binning? #15

Open AJWing opened 1 year ago

AJWing commented 1 year ago

Hello! Great tool! The approach makes complete sense to me. I was curious though, does vRhyme keep a list of the viral sequences that are not binned during the run? As you allude to, these sequences are still valuable...especially since some require no binning at all. I'm hoping there's an output of this somewhere. Any and all information would be greatly appreciated! Thank you

KrisKieft commented 1 year ago

Please see README

bio-unach commented 1 year ago

Dear Kris.

Sorry if the question is too obvious, but I can't find where de unbinned sequences are. Could you please bring some clues?

Regards.

KrisKieft commented 1 year ago

Search the README for "unbinned". A little bit down you'll see "extract_unbinned_sequences.py" which is inside the "aux" folder. This will need to be run after binning to separately pull out unbinned sequences.

bio-unach commented 1 year ago

Dear Kris, thank you so much.