dada2

Accurate, high-resolution sample inference from amplicon sequencing data

Bioconductor version: 3.23 · Package version: 1.40.0

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.

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

BiocManager::install("dada2")