dc.date.accessioned | 2021-08-16T15:31:56Z | |
dc.date.available | 2021-08-16T15:31:56Z | |
dc.date.created | 2021-08-10T16:03:58Z | |
dc.date.issued | 2021 | |
dc.identifier.citation | Mahé, Frédéric Czech, Lucas Stamatakis, Alexandros Quince, Christopher de Vargas, Colomban Dunthorn, Micah Rognes, Torbjørn . Swarm v3: towards tera-scale amplicon clustering. Bioinformatics. 2021 | |
dc.identifier.uri | http://hdl.handle.net/10852/86819 | |
dc.description.abstract | Motivation
Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes.
Results
When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic.
Availability and implementation
Source code and binaries are available at https://github.com/torognes/swarm.
Supplementary information
Supplementary data are available at Bioinformatics online. | |
dc.language | EN | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.title | Swarm v3: towards tera-scale amplicon clustering | |
dc.type | Journal article | |
dc.creator.author | Mahé, Frédéric | |
dc.creator.author | Czech, Lucas | |
dc.creator.author | Stamatakis, Alexandros | |
dc.creator.author | Quince, Christopher | |
dc.creator.author | de Vargas, Colomban | |
dc.creator.author | Dunthorn, Micah | |
dc.creator.author | Rognes, Torbjørn | |
cristin.unitcode | 185,28,0,0 | |
cristin.unitname | Naturhistorisk museum | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 2 | |
dc.identifier.cristin | 1925175 | |
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=Bioinformatics&rft.volume=&rft.spage=&rft.date=2021 | |
dc.identifier.jtitle | Bioinformatics | |
dc.identifier.pagecount | 3 | |
dc.identifier.doi | https://doi.org/10.1093/bioinformatics/btab493 | |
dc.identifier.urn | URN:NBN:no-89456 | |
dc.type.document | Tidsskriftartikkel | |
dc.type.peerreviewed | Peer reviewed | |
dc.source.issn | 1367-4803 | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/86819/1/btab493.pdf | |
dc.type.version | PublishedVersion | |
dc.relation.project | NOTUR/NORSTORE/NN9383K | |