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Swarm v2 : highly-scalable and high-resolution amplicon clustering
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Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban and Dunthorn, Micah (2015) Swarm v2 : highly-scalable and high-resolution amplicon clustering. PeerJ, 3 . e1420. doi:10.7717/peerj.1420 ISSN 2167-8359.
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Official URL: http://dx.doi.org/10.7717/peerj.1420
Abstract
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.
Item Type: | Journal Article | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||
Journal or Publication Title: | PeerJ | ||||
Publisher: | PeerJ, Ltd. | ||||
ISSN: | 2167-8359 | ||||
Official Date: | 10 December 2015 | ||||
Dates: |
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Volume: | 3 | ||||
Article Number: | e1420 | ||||
DOI: | 10.7717/peerj.1420 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Open Access (Creative Commons) |
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