Brief Communication | Published:

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Nature Methods volume 10, pages 996998 (2013) | Download Citation

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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References

  1. 1.

    Human Microbiome Project Consortium. Nature 486, 207–214 (2012).

  2. 2.

    et al. Nature 488, 86–90 (2012).

  3. 3.

    et al. Nat. Methods 10, 57–59 (2013).

  4. 4.

    et al. Nat. Methods 6, 639–641 (2009).

  5. 5.

    & Nat. Methods 7, 668–669 (2010).

  6. 6.

    , , & BMC Bioinformatics 12, 38 (2011).

  7. 7.

    , , , & Bioinformatics 27, 2194–2200 (2011).

  8. 8.

    , , & Environ. Microbiol. 12, 1889–1898 (2010).

  9. 9.

    , & PLoS ONE 6, e27310 (2011).

  10. 10.

    et al. Nat. Methods 7, 335–336 (2010).

  11. 11.

    & Numerical Taxonomy (W.H. Freeman, 1973).

  12. 12.

    et al. Genome Res. 21, 494–504 (2011).

  13. 13.

    Human Microbiome Project Consortium. Nature 486, 215–221 (2012).

  14. 14.

    et al. FEMS Microbiol. Ecol. 82, 666–677 (2012).

  15. 15.

    et al. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

  16. 16.

    , , , & BMC Bioinformatics 13, 31 (2012).

  17. 17.

    et al. Nucleic Acids Res. 40, D13–D25 (2012).

Download references

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.

Author information

Affiliations

  1. Independent Investigator, Tiburon, California, USA.

    • Robert C Edgar

Authors

  1. Search for Robert C Edgar in:

Contributions

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

Competing interests

The author declares no competing financial interests.

Corresponding author

Correspondence to Robert C Edgar.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Notes 1–3

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    Supplementary Software

    UPARSE pipeline

About this article

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DOI

https://doi.org/10.1038/nmeth.2604

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