Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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The author thanks N.A. Bokulich, J.G. Caporaso and D. Gevers for helpful discussions and providing prepublication data; P.D. Schloss for assistance with mothur; C. Quince for assistance with AmpliconNoise; L. Dethlefsen and S.M. Huse for helpful discussions; S. Yourstone for an insightful critique of a draft manuscript; and the Sloan Foundation, Microbiology of the Built Environment Program (M.L. Sogin, Marine Biological Laboratory) for providing compute resources.
The author declares no competing financial interests.
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Edgar, R. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996–998 (2013). https://doi.org/10.1038/nmeth.2604
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