Corrects amplicon errors without constructing Operational Taxonomic Units (OTUs). DADA2 is an R package that implements a quality-aware model of Illumina amplicon errors. This application is reference-free, and applicable to any genetic locus. It also implements the full amplicon workflow: filtering, dereplication, chimera identification, and merging paired-end reads. It enhances the study of microbial communities by allowing researchers to accurately reconstruct amplicon-sequenced communities at the highest resolution.