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DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods volume 13, pages 581583 (2016) | Download Citation

Abstract

We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

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Acknowledgements

We thank M. Schirmer and D. MacIntyre for productive correspondence. This work was supported by the NSF (DMS-1162538 to S.P.H.), the NIH (R01AI112401 to S.P.H.), and the Samarth Foundation (Stanford Microbiome Seed Grant to B.J.C. and S.P.H.).

Author information

Affiliations

  1. Department of Statistics, Stanford University, Stanford, California, USA.

    • Benjamin J Callahan
    •  & Susan P Holmes
  2. Second Genome, South San Francisco, California, USA.

    • Paul J McMurdie
    • , Andrew W Han
    •  & Amy Jo A Johnson
  3. Department of Applied Physics, Stanford University, Stanford, California, USA.

    • Michael J Rosen

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Contributions

B.J.C. and S.P.H. designed the research; B.J.C., P.J.M., and M.J.R. implemented the algorithm; B.J.C. performed the analysis; B.J.C., P.J.M., M.J.R., and S.P.H. wrote the paper; and A.W.H. and A.J.A.J. generated the Extreme data set designed by B.J.C., P.J.M., and A.W.H.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Benjamin J Callahan.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–8, Supplementary Tables 1–3 and Supplementary Notes 1 and 2

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    Supplementary Software

    DADA2 software package and scripts for benchmarking and analysis

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DOI

https://doi.org/10.1038/nmeth.3869

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