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bioRxiv · 10.1101/406611

Species-level microbial sequence classification is improved by source-environment information

Kaehler, B. D.·Bokulich, N.·Caporaso, J. G.·Huttley, G. A.
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Abstract

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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Kaehler, B. D., Bokulich, N., Caporaso, J. G., Huttley, G. A.. 2018-09-03. Species-level microbial sequence classification is improved by source-environment information. https://doi.org/10.1101/406611

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