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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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Question about criteria for prophages extraction #219

Closed KateSakharova closed 3 weeks ago

KateSakharova commented 1 month ago

Hello,

1) As far as I understand correctly, full sequences can also be prophages? Is there a way to extract those from VirSorter2 outputs?

2) What criteria is better to use for viruses to separate those into high confident viruses and low confident viruses?

Best, Kate

jiarong commented 3 weeks ago

Sorry, I did not notice this issue till just now.

  1. "full" suggests the whole sequence looks viral, but it just could just be a fragment from prophage. It's difficult to tell if a "full" sequence is prophage. The full sequences should have "__full" as suffix in their sequence id.
  2. viral hallmark genes.