Inconsitent taxonomic classification

I think there is a misunderstanding here. What I was trying to say is that the way SILVA taxonomy is parsed has changed. For example, the old way resulted in taxonomy strings that looked like this:

D_0__Bacteria;D_1__Actinobacteria;D_2__Actinobacteria;D_3__Actinomycetales;D_4__Actinomycetaceae;D_5__Actinomyces;D_6__Mycobacterium tuberculosis

Whereas using RESCRIPt will result in more informative taxonomy strings that look like this (i.e. similar to Greengenes):
d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;s__Mycobacterium tuberculosis

Note there is also Greengenes2, and other repositories that you can download and use via RESCRIPt, such as GTDB (can now download version 226.0), and RDP.

1 Like