title: DADA2: High-resolution sample inference from Illumina amplicon data.
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.
authors.affiliation: Department of Statistics, Stanford University, Stanford, California, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Callahan
authors.affiliation: Second Genome, South San Francisco, California, USA.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: McMurdie
authors.affiliation: Department of Applied Physics, Stanford University, Stanford, California, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Rosen
authors.affiliation: Second Genome, South San Francisco, California, USA.
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Han
authors.affiliation: Second Genome, South San Francisco, California, USA.
authors.forename: Amy Jo A
authors.initials: AJ
authors.lastname: Johnson
authors.affiliation: Department of Statistics, Stanford University, Stanford, California, USA.
authors.forename: Susan P
authors.initials: SP
authors.lastname: Holmes
mesh_terms: D000818:Animals; D015331:Cohort Studies; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D005189:False Positive Reactions; D005243:Feces / Q000382:microbiology; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007778:Lactobacillus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D051379:Mice; D064307:Microbiota / Q000235:genetics*; D011247:Pregnancy; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014621:Vagina / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S