DOI: 10.18129/B9.bioc.dada2    

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: Release (3.8)

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

Author: Benjamin Callahan <benjamin.j.callahan at>, Paul McMurdie, Susan Holmes

Maintainer: Benjamin Callahan <benjamin.j.callahan at>

Citation (from within R, enter citation("dada2")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("dada2", version = "3.8")

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biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.10.1
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License LGPL-3
Depends R (>= 3.2.0), Rcpp (>= 0.11.2), methods (>= 3.2.0)
Imports Biostrings(>= 2.42.1), ggplot2 (>= 2.1.0), data.table (>= 1.9.4), reshape2 (>= 1.4.1), ShortRead(>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges(>= 2.6.0), XVector(>= 0.16.0), BiocGenerics(>= 0.22.0)
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