To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("dada2")

In most cases, you don't need to download the package archive at all.

dada2

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 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 and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("dada2")

Documentation

HTML R Script Introduction to dada2
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 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)
LinkingTo Rcpp, RcppParallel
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements GNU make
Enhances
URL http://benjjneb.github.io/dada2/
BugReports https://github.com/benjjneb/dada2/issues
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_1.7.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) dada2_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dada2
Package Short Url http://bioconductor.org/packages/dada2/
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