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chklovski / CheckM2

Assessing the quality of metagenome-derived genome bins using machine learning
GNU General Public License v3.0
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Assessing the quality of viral bins #27

Closed quliping closed 1 year ago

quliping commented 1 year ago

Recently, I'm working on viral metagenomics. I identified viral contigs using virsorter2 and then performed binning using vRhyme. Finally I obtained some viral MAGs (vMAGs). CheckV seems could only assess the quality of single viral contig, is checkM2 worked for vMAGs?

chklovski commented 1 year ago

Hi,

In its current state CheckM2 has not been trained on viruses and will not give accurate predictions on viral bins.

LeonardoMorenoG commented 1 year ago

Hello quliping,

if you are interested in the quality assessment of your "vMAGs" (formally called UViGs, from "Uncultivated Viral Genomes") you can use a tool called CheckV (https://doi.org/10.1038/s41587-020-00774-7).

Since you mentioned you're new on viral metagenomics, I would like to recommend you the following review on computational tools for the analysis of uncultivated phage genomes: https://doi.org/10.1128/mmbr.00004-21