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 (3.15)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("dada2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.3 (R-3.3) (5.5 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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/dada2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dada2
Package Short Url https://bioconductor.org/packages/dada2/
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