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Species abundance information improves sequence taxonomy classification accuracy

View ORCID ProfileBenjamin D Kaehler, View ORCID ProfileNicholas Bokulich, View ORCID ProfileDaniel McDonald, View ORCID ProfileRob Knight, View ORCID ProfileJ Gregory Caporaso, View ORCID ProfileGavin A Huttley
doi: https://doi.org/10.1101/406611
Benjamin D Kaehler
Australian National University;
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  • For correspondence: benjamin.kaehler@anu.edu.au
Nicholas Bokulich
Northern Arizona University;
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Daniel McDonald
University of California San Diego
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Rob Knight
University of California San Diego
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J Gregory Caporaso
Northern Arizona University;
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Gavin A Huttley
Australian National University;
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  • For correspondence: gavin.huttley@anu.edu.au
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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.

Footnotes

  • Significant revision, including several new results.

  • https://library.qiime2.org/plugins/q2-clawback/

  • https://doi.org/10.5281/zenodo.2548899

  • https://doi.org/10.5281/zenodo.2549777

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 14, 2019.
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Species abundance information improves sequence taxonomy classification accuracy
Benjamin D Kaehler, Nicholas Bokulich, Daniel McDonald, Rob Knight, J Gregory Caporaso, Gavin A Huttley
bioRxiv 406611; doi: https://doi.org/10.1101/406611
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Species abundance information improves sequence taxonomy classification accuracy
Benjamin D Kaehler, Nicholas Bokulich, Daniel McDonald, Rob Knight, J Gregory Caporaso, Gavin A Huttley
bioRxiv 406611; doi: https://doi.org/10.1101/406611

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