Swarm v2: highly-scalable and high-resolution amplicon clustering

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ID: 54004
2015
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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.
Reference Key
mah2015swarmpeerj Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Mahé, Frédéric;Rognes, Torbjørn;Quince, Christopher;Vargas, Colomban de;Dunthorn, Micah;
Journal PeerJ
Year 2015
DOI
DOI not found
URL
https://peerj.com/articles/1420.pdf
Keywords
Medicine Engineering (General). Civil engineering (General) Information technology Technology Science (General) neurology. diseases of the nervous system social sciences (general) special aspects of education mathematics electronic computers. computer science industrial engineering. management engineering mining engineering. metallurgy computer software probabilities. mathematical statistics

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