dada2: Accurate, high-resolution sample inference from amplicon sequencing data

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.

Package details

AuthorBenjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes
Bioconductor views Classification ImmunoOncology Metagenomics Microbiome Sequencing
MaintainerBenjamin Callahan <benjamin.j.callahan@gmail.com>
LicenseLGPL-3
Version1.18.0
URL http://benjjneb.github.io/dada2/
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dada2")

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dada2 documentation built on Nov. 8, 2020, 6:48 p.m.