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RasmussenLab / phamb

Downstream processing of VAMB binning for Viral Elucidation
MIT License
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Running Phamb without reads #36

Closed jjensen44 closed 2 years ago

jjensen44 commented 2 years ago

Hi! Is it possible to run PHAMB on a set of contigs that lack any contributing short reads (eg just a fasta of viral contigs). From the documentation this doesn't seem possible since VAMB requires the coabundance/coverage information upstream of PHAMB- but if so would be interested in how to run correctly- thanks!

joacjo commented 2 years ago

Hi jjensen44

If you have a set of viral contigs i.e. from a metavirome sample and do not intend to run VAMB anyway, you can run a viral evaluator like CheckV on those directly. That would be my advice.

Good luck!

Best, Joachim