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Running Phamb without reads #36

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jjensen44 opened this issue Apr 26, 2022 · 1 comment
Closed

Running Phamb without reads #36

jjensen44 opened this issue Apr 26, 2022 · 1 comment

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@jjensen44
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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
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joacjo commented May 6, 2022

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

@joacjo joacjo closed this as completed Jul 11, 2022
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@joacjo @jjensen44