benjjneb/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.

Getting started

Package details

AuthorBenjamin Callahan <>, Paul McMurdie, Susan Holmes
Bioconductor views Classification ImmunoOncology Metagenomics Microbiome Sequencing
MaintainerBenjamin Callahan <>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
benjjneb/dada2 documentation built on June 2, 2024, 2:57 a.m.