Silva 138.1 taxonomy classifiers for use with QIIME 2 q2-feature-classifier

Uniform and weighted naive Bayes classifiers trained on Silva 138.1 data for use with QIIME 2 q2-feature-classifier.

full-length-average-classifier.qza and 515f-806r-average-classifier.qza are classifiers using weights averaged across 14 EMPO 3 habitat types. If in doubt, use one of these.

Original weights derived from Qiita, scripts used to derive them, and additional information available at https://github.com/BenKaehler/readytowear.

Classifiers trained on full-length 16S or 515F/806R region as labelled.

Full length Silva 138.1 reference sequences and corresponding taxonomies are in ref-seqs.qza an ref-tax.qza.

If you use any of the weighted classifiers, please cite

Kaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA. (2019). Species-level microbial sequence classification is improved by source-environment information. Nature Communications 10: 4643. doi: https://doi.org/10.1038/s41467-019-12669-6

If you use the any of the classifiers (weighted or otherwise), please cite

Bokulich, N.A., Kaehler, B.D., Rideout, J.R. et al. (2018). Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90. doi: https://doi.org/10.1186/s40168-018-0470-z

If you use any file from here, please cite:

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596

Robeson, M. S., O’Rourke, D. R., Kaehler, B. D., Ziemski, M., Dillon, M. R., Foster, J. T., & Bokulich, N. A. (2021). RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comp. Bio., 17(11). doi: https://doi.org/10.1371/journal.pcbi.1009581

Warning: Pre-trained classifiers that can be used with q2-feature-classifier currently present a security risk. If using a pre-trained classifier such as the ones provided here, you should trust the person who trained the classifier and the person who provided you with the qza file.