Hi,
I ran MetaPhlAn2 and MetaPhlAn3 together for the same sample.
v2 shows more diverse microbial communities including Bacteria, Virus and Eukaryotes where as v3 show 100% Bacteria. Which seems unreliable database. Which one should be the accurate output?
Hi @shreya
I would rely on the metaphlan 3 results since they were proved more accurate in latest evaluations https://elifesciences.org/articles/65088