Hi everyone. It might be a silly question to ask but can we use qiime pipeline for viriome metagenomics. I’m guessing everything would be same in there except taxonomy prediction?
Alternatively is there any other pipeline for viriom?
Hi @drmusk,
Virome analysis is a somewhat seperate beast from the markergene that's currently the core of qiime2 (although obviously there's oppertunities to expand this!) So, you could do your virome assembly and annotation somewehre else and import for analysis in 
, but I dont think that the marker gene pipelines here would work for you.
Best,
Justine
QIIME 2 does have a couple plugins for metagenomics, q2-metaphlan2 and q2-shogun, but I do not know whether they are appropriate for virome data.
These plugins are described in the QIIME 2 library: https://library.qiime2.org/
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