High number of bacterial genes in phamb assembled bins about phamb HOT 3 CLOSED

Hi Shail

The reason for running CheckV is to identify reliable viral-bins, therefore we recommend to only consider Medium and High-quality bins for further analysis (those based on the AAI-model). Low-quality shall always be considered with a lot of scepticism.

As for "Complete-bins" I checked your quality file, which had 4 examples, I see in those that a lot of sequence has been removed by CheckV. Perhaps you wanna evaluate the resulting cleaned sequences by CheckV.

Best,
Joachim

from phamb.

Thank you for your prompt response.
Yes, only medium and high quality bins will be used for further analysis.
I'll re-run checkv on cleaned fasta files (checkv output from the first run) and let you know how it goes.

from phamb.

I ran CheckV again and found that the high number of bacterial genes was mostly in quality bins (high and medium) identified by the HMM-based (lower-bound) model of CheckV.

from phamb.