DADA2 package



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 can resolve sequence variants that differ by as little as one nucleotide.


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 (fastqFilter, fastqPairedFilter)

  • Dereplication (derepFastq)

  • Sample Inference (dada)

  • Chimera Removal (isBimeraDenovo, removeBimeraDenovo)

  • Merging of Paired Reads (mergePairs)

  • Taxonomic Classification (assignTaxonomy)


Benjamin Callahan

Paul J McMurdie II

Michael Rosen

Susan Holmes

Want to suggest features or report bugs for Use the GitHub issue tracker.