dada2

DOI: 10.18129/B9.bioc.dada2  

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction to dada2
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 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)
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	Rbec
Suggests Me	mia
Links To Me
Build Report

Package Archives

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

Source Package	dada2_1.26.0.tar.gz
Windows Binary	dada2_1.26.0.zip (64-bit only)
macOS Binary (x86_64)	dada2_1.26.0.tgz
macOS Binary (arm64)	dada2_1.26.0.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