Prophage tools - Githubissues

replikation / What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

https://mult1fractal.github.io/wtp-documentation/

GNU General Public License v3.0

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Prophage tools #114

Closed ibelalov closed 3 years ago

ibelalov commented 3 years ago

README says: Proper prophage detection is not implemented (yet) - but a handful of tools report them - so they are mostly identified

What are those tools, other than phigaro? What programs contribute to 'Provirus' column in the reports file?

mult1fractal commented 3 years ago

prophage detection tools could be:

Phaster
Virsorter
Phage_Finder
ProphET
Prophinder
PhiSpy

but I didn't tested/checked them yet. this was our plan for next year

I guess with reports file you mean the all_pos_phage_quality_summary.tsv from here at the bottom of the page (otherwise please specify or paste your output here). This is just the output from checkV

ibelalov commented 3 years ago

Thanks. Got it