DADA2: High-resolution Sample Inference From Illumina Amplicon Data

Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cohort Studies
  • Computational Biology / methods*
  • DNA, Bacterial / genetics
  • False Positive Reactions
  • Feces / microbiology
  • Female
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Lactobacillus / classification
  • Lactobacillus / genetics
  • Lactobacillus / isolation & purification*
  • Mice
  • Microbiota / genetics*
  • Pregnancy
  • RNA, Ribosomal, 16S / genetics
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*
  • Software*
  • Vagina / microbiology

Substances

  • DNA, Bacterial
  • RNA, Ribosomal, 16S