Entering edit mode
23 months ago
ramin.k2013
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0
I am using metaphlan3 for creating relative abundance profile of bacteria and viruses in faecal metagenomics samples. Looking at the abundance profiles of 3 donors, none of them contain crassphage which is against the literature (crassphage comprises up to 90% of the gut virome). However, kraken2 results were consistent with what I expected. I am wondering what the issue is with metaphlan3 and whether it is a reliable pipeline for viral metagenomics as well as for bacteria.