6395539
doi
10.5281/zenodo.6395539
oai:zenodo.org:6395539
Silva 138.1 taxonomy classifiers for use with QIIME 2 q2-feature-classifier
Kaehler, Benjamin D
University of New South Wales
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
<p>Uniform and weighted naive Bayes classifiers trained on Silva 138.1 data for use with QIIME 2 q2-feature-classifier.</p>
<p>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.</p>
<p>Original weights derived from <a href="https://qiita.ucsd.edu/">Qiita</a>, scripts used to derive them, and additional information available at <a href="https://github.com/BenKaehler/readytowear">https://github.com/BenKaehler/readytowear</a>.</p>
<p>Classifiers trained on full-length 16S or 515F/806R region as labelled.</p>
<p>Full length Silva 138.1 reference sequences and corresponding taxonomies are in ref-seqs.qza an ref-tax.qza.</p>
<p>If you use any of the weighted classifiers, please cite</p>
<ul>
<li>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: <a href="https://doi.org/10.1038/s41467-019-12669-6">https://doi.org/10.1038/s41467-019-12669-6</a></li>
</ul>
<p>If you use the any of the classifiers (weighted or otherwise), please cite</p>
<ul>
<li>
<p>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: <a href="https://doi.org/10.1186/s40168-018-0470-z">https://doi.org/10.1186/s40168-018-0470-z</a></p>
</li>
</ul>
<p>If you use any file from here, please cite:</p>
<ul>
<li>
<p>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. <em>Nucl. Acids Res</em>. 41 (D1): D590-D596</p>
</li>
<li>
<p>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. <em>PLoS Comp. Bio.</em>, <em>17</em>(11). doi: <a href="https://doi.org/10.1371/journal.pcbi.1009581">https://doi.org/10.1371/journal.pcbi.1009581</a></p>
</li>
</ul>
<p>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.</p>
Zenodo
2022-03-30
info:eu-repo/semantics/other
6395538
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