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

[AJWing]

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]

Please see README

[bio-unach]

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]

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]

Dear Kris, thank you so much.