RT Journal Article
SR Electronic
T1 Species abundance information improves sequence taxonomy classification accuracy
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 406611
DO 10.1101/406611
A1 Benjamin D. Kaehler
A1 Nicholas A. Bokulich
A1 Daniel McDonald
A1 Rob Knight
A1 J. Gregory Caporaso
A1 Gavin A. Huttley
YR 2019
UL http://biorxiv.org/content/early/2019/02/14/406611.abstract
AB 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.