dada2

DOI: 10.18129/B9.bioc.dada2    

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: Release (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>

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	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 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
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Build Report

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
Package Short Url	http://bioconductor.org/packages/dada2/
Package Downloads Report	Download Stats