DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods volume 13, pages581–583(2016)Cite this article

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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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Figure 1: Comparison of sequence variants inferred by DADA2 with OTUs constructed by UPARSE.
Figure 2: L.crispatus sequence variants in the human vaginal community during pregnancy.

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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.).

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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

Authors
  1. Benjamin J Callahan
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  2. Paul J McMurdie
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  3. Michael J Rosen
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  4. Andrew W Han
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  5. Amy Jo A Johnson
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  6. Susan P Holmes
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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.

Corresponding author

Correspondence to Benjamin J Callahan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 1–3 and Supplementary Notes 1 and 2 (PDF 1809 kb)

Supplementary Software

DADA2 software package and scripts for benchmarking and analysis (ZIP 1312 kb)

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Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016). https://doi.org/10.1038/nmeth.3869

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