Hello MetaPhlAn community
I am a bit confused about the new virus detection pipeline in metaphlan4.1. Usually, we are interested in the abundance of a certain taxon in a metagenomic sample. In the case of virus detection, I am interested in the relative abundance of certain viruses compared to the whole sample. However, the viral detection module is somewhat isolated. I get the coverage & breadth for each virus reference but it’s not integrated into the main profiling analysis. Do you have plans to integrate this so that I get a single profile per sample where also viruses are considered?
How do you suggest to continue with the version now in order to get the relative abundance of the viral taxa in the same format as the bacterial taxa? I see the following issues:
-
The format of the virus taxonomy is different to the rest (e.g. not d__[…];k__[…];etc. We rather have something like: NC_007924_Lactobacillus_phage_KC5a
-
The statistics is either breadth, or mean/median coverage. However, this does not easily translate to relative abundance. How would you suggest to use those numbers?