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DADA2: High-resolution sample inference from Illumina amplicon data

2016; Nature Portfolio; Volume: 13; Issue: 7 Linguagem: Inglês

10.1038/nmeth.3869

1548-7105

Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen, Andrew Han, Amy Jo A Johnson, Susan Holmes,

Reproductive tract infections research

DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide. 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.