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Bioconductor - dada2 (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dada2")
Details biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software Version 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License LGPL-2 Depends R (>= 4.1.0), 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) System Requirements GNU make URL http://benjjneb.github.io/dada2/ Bug Reports https://github.com/benjjneb/dada2/issues See More Package Archives

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

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