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Species abundance information improves sequence taxonomy classification accuracy

By Benjamin D. Kaehler, Nicholas A. Bokulich, Daniel McDonald, Rob Knight, J. Gregory Caporaso, Gavin A. Huttley

Posted 03 Sep 2018
bioRxiv DOI: 10.1101/406611 (published DOI: 10.1038/s41467-019-12669-6)

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate that species-level resolution is attainable.

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