creating a 12-rank SILVA taxonomy with RESCRIPt

[SoilRotifer (Mike Robeson)]

Hi @aeriel.belk,

@aeriel.belk

I have a quick question. I want to use the silva reference with the 12-rank taxonomy, not the 7-rank like this tutorial references.

We had recently updated our SILVA taxonomy parser to allow you to select the exact taxonomy ranks you'd like to use via the --p-ranks flag. You can select these ranks for either the parse-silva-taxonomy or get-silva-data actions:

That is, you can use this flag like so:

qiime rescript get-silva-data \
    --p-rank-propagation \
    --p-include-species-labels \
    --p-ranks domain kingdom phylum class subclass order family genus \
    --output-dir ... 

or

qiime rescript parse-silva-taxonomy \
    --p-rank-propagation \
    --p-include-species-labels \
    --p-ranks domain kingdom phylum class subclass order family genus \
    --output-dir ... 

You can re-install RESCRIPt following the instructions here. Note you'll need to be running QIIME version 2020.8.

I hope to update parts of the tutorial soon.

-Let us know how it goes!
-Mike