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

DADA2: High-resolution sample inference from Illumina amplicon data.

Author information

1
Department of Statistics, Stanford University, Stanford, California, USA.
2
Second Genome, South San Francisco, California, USA.
3
Department of Applied Physics, Stanford University, Stanford, California, USA.

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.

PMID:
27214047
PMCID:
PMC4927377
DOI:
10.1038/nmeth.3869
[Indexed for MEDLINE]
Free PMC Article

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