The newest version of metaphlan4 allows for viral detection. Is it possible to do this within humann3 with a flag? when I check the -h for humann, I don’t see a virus flag. I would need to update my humann version with the new chocophlan databases of course. Thanks! And your tools are amazing, thank you!
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HUMAnN does not contain pangenomes for potential viruses detected by MetaPhlAn, so it’s not possible to profile their genes by the traditional HUMAnN workflow. Notably, viral reads DO map to proteins during the translated search stage, so you can often make inferences about viral behavior from those data (looking up the UniRef90/50s with viral source taxonomy).