Comments (3)
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
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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.
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