SILVA 128 classifiers available for download

feature-classifier

(Greg Caporaso) #1

I created Silva 128 99% OTU classifiers trained on full length sequences and on the 515F/806R region only. These are derived from the QIIME-compatible SILVA release for SILVA 128.

You can find these files in Dropbox for now, and we’ll link these (or more recent classifiers if they’re available) from the data resources page for the 2018.4 release.

The most relevant files are:

  • silva-128-99-nb-classifier.qza : trained on full-length 99% OTU representative sequences, and the SILVA_128_QIIME_release/taxonomy/taxonomy_all/99/taxonomy_all_levels.txt taxonomy file
  • silva-128-99-515-806-nb-classifier.qza : trained on 99% OTU representative sequences, trimmed to the region bound by the 515/806 primers, , and the SILVA_128_QIIME_release/taxonomy/taxonomy_all/99/taxonomy_all_levels.txt taxonomy file

Those are prepared in the same way that we prepared classifiers for the SILVA 119 release.

For experimental purposes, I also trained these classifiers on the the SILVA_128_QIIME_release/taxonomy/taxonomy_all/99/majority-taxonomy-7-levels.txt and the SILVA_128_QIIME_release/taxonomy/taxonomy_all/99/consensus-taxonomy-7-levels.txt files, to experiment with these. These are files that collapse the full SILVA taxonomy to exactly seven levels (domain, phylum, class, order, family, genus, and species), so may be easier to interpret than the others. I’m interested to hear whether folks think these files are useful.


SILVA 132 for qiime
SILVA classifier taxonomy
(Nicholas Bokulich) #5

An off-topic reply has been split into a new topic: SILVA classifier taxonomy

Please keep replies on-topic in the future.