To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dada2")

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dada2

DOI: 10.18129/B9.bioc.dada2    

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: Release (3.5)

The dada2 package infers exact sequence variants (SVs) from amplicon 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.

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("https://bioconductor.org/biocLite.R")
biocLite("dada2")

Documentation

HTML R Script Introduction to dada2
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.4.0
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(>= 2.32.1), ggplot2 (>= 2.1.0), data.table (>= 1.9.4), reshape2 (>= 1.4.1), ShortRead(>= 1.24.0), 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.

Package Source dada2_1.4.0.tar.gz
Windows Binary dada2_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) dada2_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dada2
Package Short Url http://bioconductor.org/packages/dada2/
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