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 <>, Paul McMurdie, Susan Holmes
Bioconductor views Classification ImmunoOncology Metagenomics Microbiome Sequencing
MaintainerBenjamin Callahan <>
Package repositoryView on Bioconductor
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dada2 documentation built on April 29, 2020, 2:30 a.m.