Description

The dada2 package is centered around the DADA2 algorithm for accurate high-resolution of sample composition from amplicon sequencing data. The DADA2 algorithm is both more sensitive and more specific than commonly used OTU methods, and resolves amplicon sequence variants (ASVs) that differ by as little as one nucleotide.

Details

The dada2 package also provides a full set of tools for taking raw amplicon sequencing data all the way through to a feature table representing sample composition. Provided facilities include:

• Quality filtering (filterAndTrim, fastqFilter, fastqPairedFilter)

• Dereplication (derepFastq)

• Learn error rates (learnErrors)

• Sample Inference (dada)

• Chimera Removal (removeBimeraDenovo, isBimeraDenovo, isBimeraDenovoTable)

• Merging of Paired Reads (mergePairs)

• Taxonomic Classification (assignTaxonomy, assignSpecies)

Author(s)

Benjamin Callahan benjamin.j.callahan@gmail.com

Paul J McMurdie II mcmurdie@stanford.edu

Michael Rosen eigenrosen@gmail.com

Susan Holmes susan@stat.stanford.edu