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PeerJ. 2015 Dec 10;3:e1420. doi: 10.7717/peerj.1420. eCollection 2015.

Swarm v2: highly-scalable and high-resolution amplicon clustering.

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Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany.
Department of Informatics, University of Oslo , Oslo , Norway ; Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway.
Warwick Medical School, University of Warwick , Warwick , United Kingdom.
UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, CNRS , Roscoff , France ; UMR7144 Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06 , Roscoff , France.


Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.


Barcoding; Environmental diversity; Molecular operational taxonomic units

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