dada2

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see dada2.

Accurate, high-resolution sample inference from amplicon sequencing data


Bioconductor version: 3.6

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 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 "3.4") 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

Reference Manual PDF
NEWS Text

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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)
System Requirements GNU make
URL http://benjjneb.github.io/dada2/
Bug Reports https://github.com/benjjneb/dada2/issues
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Suggests BiocStyle, knitr, rmarkdown
Linking To Rcpp, RcppParallel
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Package Archives

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

Source Package dada2_1.6.0.tar.gz
Windows Binary dada2_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) dada2_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dada2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dada2
Package Short Url https://bioconductor.org/packages/dada2/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive