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UPARSE: highly accurate OTU sequences from microbial amplicon reads

Abstract

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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Figure 1: Results on 16S mock communities.
Figure 2: Results on Human Microbiome Project (HMP) data sets.

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Acknowledgements

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.

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R.C.E. conceived of the study, performed the analysis and wrote the manuscript.

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Correspondence to Robert C Edgar.

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The author declares no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 1–3 (PDF 1505 kb)

Supplementary Software

UPARSE pipeline (TAR 1350 kb)

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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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