Which file to use to train the classifier?

[Nicholas_Bokulich]

Hi @Niyuh ,

The process of building a reference sequence database can be complicated! So there is a QIIME 2 plugin (RESCRIPt) to automate this process, including from SILVA. Please see this tutorial:

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 construc…

The sequences, taxonomy, and pre-trained classifiers prepared using the RESCRIPt plugin as described in this tutorial are also available on the QIIME 2 website data resources page: Data resources — QIIME 2 2024.2.0 documentation