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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
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 | ||||
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Journal or Publication Title: | PeerJ | ||||
| Publisher: | PeerJ, Ltd. | ||||
| ISSN: | 2167-8359 | ||||
| Official Date: | 25 September 2014 | ||||
| Dates: |
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| 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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