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dada2

Accurate, high-resolution sample inference from amplicon sequencing data


Bioconductor version: Release (3.19)

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 gmail.com>, Paul McMurdie, Susan Holmes

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

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dada2")

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

Documentation

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

browseVignettes("dada2")
Introduction to dada2 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.32.0
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
URL http://benjjneb.github.io/dada2/
Bug Reports https://github.com/benjjneb/dada2/issues
See More
Suggests BiocStyle, knitr, rmarkdown
Linking To Rcpp, RcppParallel
Enhances
Depends On Me MiscMetabar
Imports Me Rbec, DBTC
Suggests Me mia
Links To Me
Build Report Build Report

Package Archives

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

Source Package dada2_1.32.0.tar.gz
Windows Binary dada2_1.32.0.zip
macOS Binary (x86_64) dada2_1.32.0.tgz
macOS Binary (arm64) dada2_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dada2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dada2
Bioc Package Browser https://code.bioconductor.org/browse/dada2/
Package Short Url https://bioconductor.org/packages/dada2/
Package Downloads Report Download Stats