DOI: 10.18129/B9.bioc.dada2    

This is the development version of dada2; for the stable release version, see dada2.

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: Development (3.7)

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 genus-species assignment 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 and enter:

## try http:// if https:// URLs are not supported


HTML R Script Introduction to dada2
PDF   Reference Manual
Text   NEWS


biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.7.6
In Bioconductor since BioC 3.3 (R-3.3) (2 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)
LinkingTo Rcpp, RcppParallel
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements GNU make
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package dada2_1.7.6.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) dada2_1.7.6.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: