Suggestion : add checkv step beforehand to remove complete genomes about phamb HOT 2 OPEN

Regarding the above issue, I have found a few hundred contigs representing complete viral genomes (based off CheckV - DTR presence and high confidence only). I am using both VAMB and PHAMB. My questions are:

1. When would be the best time to remove these contigs from the dataset?
2. When would be the best time to add them back in (and how)?

from phamb.

Hi Greg

Yes, I have seen cases where VAMB clustering results in complete virus contigs (DTR presence) are binned with unrelated contigs (not very frequent though), i.e. bin contamination. Based on your results, it looks like it is a matter of 557-351=206 complete virus contigs that ends up in a HQ bin, is my interpretation correct?

• I think you're absolutely right that an option would be to run a prior search on the individual contigs for the presence of complete virus contigs (i.e. a DTR search) then remove them from the set going into phamb. However, that would mean you end up running CheckV twice, which turns into a lot of computation time + money.
• An alternative idea that I would appreciate as a user, would be to scan viral bins for the presence of DTR's (complete virus contigs) then extract the complete virus and discard the "contaminating" contigs. Howver, if the discarded contigs frequently represents virus sequences this solution is not ideal.

I would appreciate your thoughts on this, thanks!

Best,
Joachim

from phamb.