Reference database (97%) for qiime vsearch cluster-features-closed-reference

[PatoUru]

Hi all!
I would like to know where could I get the 97_otus.qza from silva 138
Thank you very much!!

qiime vsearch cluster-features-closed-reference --i-table feature-table.qza --i-sequences rep-set.qza --i-reference-sequences 97_otus.qza --o-clustered-table closed-0.97-feature-table.qza --o-clustered-sequences closed-0.97clustered-seqs.qza --o-unmatched-sequences closed-unmatched-sequences.qza --p-perc-identity 0.97 --p-strand both --p-threads 15

[Nicholas_Bokulich]

Hi @PatoUru,

@PatoUru

I would like to know where could I get the 97_otus.qza from silva 138

You will need to make it yourself! We supply a set of files that we pre-processed with RESCRIPt, including the SILVA 138 99% reference files on the Q2 data resources page, which you can use as a starting point.

This tutorial describes how we prepared those files, as well as how you could prepare the 97% OTUs. You should be able to just re-cluster the 99% OTUs to generate a 97% OTUs file, see the command in this section:

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…