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>

Citation (from within R, enter citation("dada2")):

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

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