@article{
 title = {Swarm v2: highly-scalable and high-resolution amplicon clustering},
 type = {article},
 year = {2015},
 identifiers = {[object Object]},
 pages = {e1420},
 volume = {3},
 websites = {https://peerj.com/articles/1420/},
 id = {94f32b50-bd92-3cfd-833e-ba99d4d61ff9},
 created = {2016-02-25T16:48:20.000Z},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2016-02-25T17:05:07.000Z},
 tags = {2015,sbr_phyto_eppo},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 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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