dc.date.accessioned | 2018-02-14T19:07:51Z | |
dc.date.available | 2018-02-14T19:07:51Z | |
dc.date.created | 2015-12-10T10:55:55Z | |
dc.date.issued | 2015 | |
dc.identifier.citation | Mahé, Frédéric Rognes, Torbjørn Quince, Christopher de Vargas, Colomban Dunthorn, Micah . Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. 2015, 3 | |
dc.identifier.uri | http://hdl.handle.net/10852/60119 | |
dc.description.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. | en_US |
dc.language | EN | |
dc.language.iso | en | en_US |
dc.publisher | PeerJ Inc. | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.title | Swarm v2: highly-scalable and high-resolution amplicon clustering | en_US |
dc.type | Journal article | en_US |
dc.creator.author | Mahé, Frédéric | |
dc.creator.author | Rognes, Torbjørn | |
dc.creator.author | Quince, Christopher | |
dc.creator.author | de Vargas, Colomban | |
dc.creator.author | Dunthorn, Micah | |
cristin.unitcode | 185,15,5,35 | |
cristin.unitname | Forskningsgruppen for biomedisinsk informatikk | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 1 | |
dc.identifier.cristin | 1299218 | |
dc.identifier.bibliographiccitation | info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PeerJ&rft.volume=3&rft.spage=&rft.date=2015 | |
dc.identifier.jtitle | PeerJ | |
dc.identifier.volume | 3 | |
dc.identifier.pagecount | 12 | |
dc.identifier.doi | http://dx.doi.org/10.7717/peerj.1420 | |
dc.identifier.urn | URN:NBN:no-62756 | |
dc.type.document | Tidsskriftartikkel | en_US |
dc.type.peerreviewed | Peer reviewed | |
dc.source.issn | 2167-8359 | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/60119/2/2015%2BMah%25C3%25A9-PeerJ59423.pdf | |
dc.type.version | PublishedVersion | |
cristin.articleid | e1420 | |