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Swarm : robust and fast clustering method for amplicon-based studies

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Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2014) Swarm : robust and fast clustering method for amplicon-based studies. PeerJ, 2 . e593. doi:10.7717/peerj.593

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Official URL: http://dx.doi.org/10.7717/peerj.593

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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.

Item Type: Journal Article
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
Journal or Publication Title: PeerJ
Publisher: PeerJ, Ltd.
ISSN: 2167-8359
Official Date: 25 September 2014
Dates:
DateEvent
25 September 2014Published
Volume: 2
Article Number: e593
DOI: 10.7717/peerj.593
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access

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