Please cite swarm as follows:

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2:e593 <http://dx.doi.org/10.7717/peerj.593>


Bibtex format:

@article{10.7717/peerj.593,
 title = {Swarm: robust and fast clustering method for amplicon-based studies},
 author = {Mahé, Frédéric and Rognes, Torbjørn and Quince, Christopher and de Vargas, Colomban and Dunthorn, Micah},
 year = {2014},
 month = {9},
 keywords = {Environmental diversity, Barcoding, Molecular operational taxonomic units},
 abstract = {Popular \textit{de novo} amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.},
 volume = {2},
 pages = {e593},
 journal = {PeerJ},
 issn = {2167-8359},
 url = {http://dx.doi.org/10.7717/peerj.593},
 doi = {10.7717/peerj.593}
}
