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

Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2014) Swarm:Robust and fast clustering method for amplicon-based studies. PeerJ, 2014 (1). ISSN 2167-8359

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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. Swarmwas 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: Article
Additional Information: Publisher Copyright: © 2014 Mahé et al.
Uncontrolled Keywords: barcoding,environmental diversity,molecular operational taxonomic units,neuroscience(all),biochemistry, genetics and molecular biology(all),agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/2800
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 09 Sep 2022 14:30
Last Modified: 22 Sep 2022 19:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/88040
DOI: 10.7717/peerj.593

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