Swarm v2: highly-scalable and high-resolution amplicon clustering. Mahé​, F.; Rognes​, T.; Quince, C.; de Vargas, C.; and Dunthorn, M. PeerJ, 3:e1420, 2015.
Swarm v2: highly-scalable and high-resolution amplicon clustering [link]Website  abstract   bibtex   
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. Swarmv1 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 chainedOTUs.Herewe present Swarmv2,which has two important novel features: (1) a newalgorithm for d =1 that allows the computation time of the program to scale linearlywith increasing amounts of data; and (2) the newfastidious option that reduces under-grouping by grafting lowabundantOTUs (e.g., singletons and doubletons) onto larger ones. Swarmv2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputsOTU repre- sentatives in fasta format, and plots individualOTUs as two-dimensional networks. Submitted
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 title = {Swarm v2: highly-scalable and high-resolution amplicon clustering},
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 year = {2015},
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 pages = {e1420},
 volume = {3},
 websites = {https://peerj.com/articles/1420/},
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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. Swarmv1 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 chainedOTUs.Herewe present Swarmv2,which has two important novel features: (1) a newalgorithm for d =1 that allows the computation time of the program to scale linearlywith increasing amounts of data; and (2) the newfastidious option that reduces under-grouping by grafting lowabundantOTUs (e.g., singletons and doubletons) onto larger ones. Swarmv2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputsOTU repre- sentatives in fasta format, and plots individualOTUs as two-dimensional networks. Submitted},
 bibtype = {article},
 author = {Mahé​, Frédéric and Rognes​, Torbjørn and Quince, Christopher and de Vargas, Colomban and Dunthorn, Micah},
 journal = {PeerJ}
}
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