Creating A SILVA Classifier

[Nicholas_Bokulich]

HI @gpgarcia,

@gpgarcia

The current version of the Silva Classifier posted to the documents page is not compatible with my current version of QIIME 2 (2020.2)

This is because you are running an old version of QIIME 2! I recommend just installing the latest version if you can.

@gpgarcia

I am trying to follow the Mike Robeson code on github

If you notice, the README on that repo notes that that has been superceded by another repository, which has been superceded by RESCRIPt.

And the great @SoilRotifer himself recently wrote a tutorial for using this new plugin to create a SILVA classifier:

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…

Though the QIIME 2 data-resources page also hosts some pre-formatted SILVA sequences and taxonomies that you can use to train a classifier, no need to follow that whole tutorial.

But the easiest thing of all would be to install the latest version of QIIME 2 so that you can use the latest pre-trained classifiers.

Good luck!