Mahé, F., Rognes, T., Quince, C., de Vargas, C. and Dunthorn, M. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ, 2(e593), (doi: 10.7717/peerj.593) (PMID:25276506)
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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: | Articles |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Quince, Dr Christopher |
Authors: | Mahé, F., Rognes, T., Quince, C., de Vargas, C., and Dunthorn, M. |
College/School: | College of Science and Engineering > School of Engineering |
Journal Name: | PeerJ |
Publisher: | PeerJ |
ISSN: | 2167-8359 |
ISSN (Online): | 2167-8359 |
Copyright Holders: | Copyright © 2014 The Authors |
First Published: | First published in PeerJ 2:e593 |
Publisher Policy: | Reproduced under a Creative Commons License |
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