title: Swarm: robust and fast clustering method for amplicon-based studies.
abstract: Popular 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.
authors.affiliation: CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France ; Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Mahé
authors.affiliation: Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway ; Department of Informatics, University of Oslo , Oslo , Norway.
authors.forename: Torbjørn
authors.initials: T
authors.lastname: Rognes
authors.affiliation: School of Engineering, University of Glasgow , Glasgow , UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Quince
authors.affiliation: CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.affiliation: Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany.
authors.forename: Micah
authors.initials: M
authors.lastname: Dunthorn
keywords: Barcoding; Environmental diversity; Molecular operational taxonomic units