To cite package ‘dada2’ in publications use:

  Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP
  (2016). “DADA2: High-resolution sample inference from Illumina
  amplicon data.” _Nature Methods_, *13*, 581-583.
  doi:10.1038/nmeth.3869 <https://doi.org/10.1038/nmeth.3869>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {DADA2: High-resolution sample inference from Illumina amplicon data},
    author = {Benjamin J Callahan and Paul J McMurdie and Michael J Rosen and Andrew W Han and Amy Jo A Johnson and Susan P Holmes},
    journal = {Nature Methods},
    volume = {13},
    pages = {581-583},
    year = {2016},
    doi = {10.1038/nmeth.3869},
  }