Pretrained SILVA 138.1 classifiers (weighted and uniform), reference dbs, and habitat weights

Pretrained SILVA 138.1 classifiers for use with q2-feature-classifier are now available on Zenodo.

You can download classifiers for full-length 16S or 515f-806r (V4) trimmed reads. There are uniform classifiers and classifiers weighted for animal-distal-gut, animal-surface, animal-secretion, soil-non-saline, or animal-corpus EMPO 3 habitat types. There are also weighted classifiers for human-oral or human-stool samples.

There are also "average" weighted classifiers that use weights averaged across 14 EMPO 3 habitat types. We found that those generally outperformed uniform (ie. unweighted) classifiers. The habitat-specific classifiers were even better.

If you have samples from a range of other EMPO 3 habitat types, you can train your own custom weighted SILVA 138.1 classifier using weights and reference databases available at readytowear.