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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 (3.20)

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 "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to dada2 HTML R Script
Reference Manual PDF


biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License LGPL-2
Depends R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0)
Imports Biostrings(>= 2.42.1), ggplot2 (>= 2.1.0), 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)
System Requirements GNU make
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Imports Me Rbec, DBTC
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Source Package dada2_1.33.0.tar.gz
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