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UPARSE: highly accurate OTU sequences from microbial amplicon reads

Nature Methods volume 10, pages 996–998 (2013)Cite this article

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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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References

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

  2. Lundberg, D.S. et al. Nature 488, 86–90 (2012).

    Article  CAS  Google Scholar 

  3. Bokulich, N.A. et al. Nat. Methods 10, 57–59 (2013).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  5. Reeder, J. & Knight, R. Nat. Methods 7, 668–669 (2010).

    Article  CAS  Google Scholar 

  6. Quince, C., Lanzen, A., Davenport, R.J. & Turnbaugh, P.J. BMC Bioinformatics 12, 38 (2011).

    Article  Google Scholar 

  7. Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. & Knight, R. Bioinformatics 27, 2194–2200 (2011).

    Article  CAS  Google Scholar 

  8. Huse, S.M., Welch, D.M., Morrison, H.G. & Sogin, M.L. Environ. Microbiol. 12, 1889–1898 (2010).

    Article  CAS  Google Scholar 

  9. Schloss, P.D., Gevers, D. & Westcott, S.L. PLoS ONE 6, e27310 (2011).

    Article  CAS  Google Scholar 

  10. Caporaso, J.G. et al. Nat. Methods 7, 335–336 (2010).

    Article  CAS  Google Scholar 

  11. Sneath, P.H.A. & Sokal, R.R. Numerical Taxonomy (W.H. Freeman, 1973).

  12. Haas, B.J. et al. Genome Res. 21, 494–504 (2011).

    Article  CAS  Google Scholar 

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

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

    Article  CAS  Google Scholar 

  15. DeSantis, T.Z. et al. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

    Article  CAS  Google Scholar 

  16. Masella, A.P., Bartram, A.K., Truszkowski, J.M., Brown, D.G. & Neufeld, J.D. BMC Bioinformatics 13, 31 (2012).

    Article  CAS  Google Scholar 

  17. Sayers, E.W. et al. Nucleic Acids Res. 40, D13–D25 (2012).

    Article  CAS  Google Scholar 

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.

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Authors and Affiliations

  1. Independent Investigator, Tiburon, California, USA

    Robert C Edgar

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  1. Robert C Edgar
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Contributions

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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