DADA2: High-resolution sample inference from Illumina amplicon data
Open Access
- 23 May 2016
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 13 (7), 581-583
- https://doi.org/10.1038/nmeth.3869
Abstract
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.This publication has 23 references indexed in Scilit:
- Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad nicheScience, 2015
- The gut microbiota era marches onNature Reviews Gastroenterology & Hepatology, 2014
- Oligotyping analysis of the human oral microbiomeProceedings of the National Academy of Sciences of the United States of America, 2014
- UPARSE: highly accurate OTU sequences from microbial amplicon readsNature Methods, 2013
- Structure, function and diversity of the healthy human microbiomeNature, 2012
- Fast, accurate error-correction of amplicon pyrosequences using AcaciaNature Methods, 2012
- Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsThe ISME Journal, 2012
- UCHIME improves sensitivity and speed of chimera detectionBioinformatics, 2011
- Removing Noise From Pyrosequenced AmpliconsBMC Bioinformatics, 2011
- Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributionsNature Methods, 2010