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RasmussenLab / phamb

Downstream processing of VAMB binning for Viral Elucidation
MIT License
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Vcheck on predicted viral bins #35

Closed barbarashih closed 1 year ago

barbarashih commented 2 years ago

I got a single Concatenated predicted viral bin from RF model in resultsdir/vamb_bins. Do I input this single file in checkV? How would checkV know which contigs belong to the same bin (or does that now matter at this stage?)

Thank you

Barbara

joacjo commented 2 years ago

Hi Barbara

The output produced by the workflow concatenates the contigs of a bin into one sequence that can be evaluated with CheckV directly - so yes you input that single file with checkV to evaluate the quality of the predicted viral bin :-)

Best, Joachim

CHENGuowei-cityu commented 2 years ago

Hello Joachim, Could you please talk more about the concatenation of sequences in a bin? How does the program perform it? By what standard?

Thank you, Guowei

joacjo commented 2 years ago

Hello Guowei

Like with bacterial MAGs, the sequential order of the contigs in a viral bin/viral MAG is not known. Unless you find a reference genome to guide how to put the genome/contigs puzzle together, even though mosaicism in viruses may hinder this effort. The contigs are, by choice, not connected by gaps like "XXX" or some other accepted DNA character in fasta-files as it might mess up the viral evaluation machinery of CheckV.

Best, Joachim

joacjo commented 1 year ago

No activity on this one, closing it.