joacjo
commented
2 years ago 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
kellifeeser
Hi, I compared the results that I obtained using vibrant contigs before and after running phamb using checkv
After
Where mean is the mean of contig length, sum is the total length of all contigs and max is the maximum size of the biggest “virus”.
This suggests to me that phamb wants to combine contigs even if they are considered "complete". Maybe adding a checkv step beforehand to remove the complete ones from the phamb analysis could be useful?