The Library
Swarm v3 : towards tera-scale amplicon clustering
Tools
Mahé, Frédéric, Czech, Lucas, Stamatakis, Alexandros, Quince, Christopher , de Vargas, Colomban, Dunthorn, Micah and Rognes, Torbjørn (2022) Swarm v3 : towards tera-scale amplicon clustering. Bioinformatics, 38 (1). pp. 267-269. doi:10.1093/bioinformatics/btab493 ISSN 1367-4803.
|
PDF
WRAP-Swarm-v3-towards-tera-scale-amplicon-yclustering-Quince-2022.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (220Kb) | Preview |
Official URL: https://doi.org/10.1093/bioinformatics/btab493
Abstract
Motivation Previously we presented swarm, an open-source amplicon clustering program 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 to 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. z
Availability Source code and binaries are available at https://github.com/torognes/swarm
Supplementary information Supplementary data are available at Bioinformatics online.
Item Type: | Journal Article | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subjects: | Q Science > Q Science (General) | ||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||||||||||
SWORD Depositor: | Library Publications Router | ||||||||||||
Library of Congress Subject Headings (LCSH): | Swarm intelligence, Bioinformatics, Computer algorithms, Natural computation | ||||||||||||
Journal or Publication Title: | Bioinformatics | ||||||||||||
Publisher: | Oxford University Press | ||||||||||||
ISSN: | 1367-4803 | ||||||||||||
Official Date: | 1 January 2022 | ||||||||||||
Dates: |
|
||||||||||||
Volume: | 38 | ||||||||||||
Number: | 1 | ||||||||||||
Page Range: | pp. 267-269 | ||||||||||||
DOI: | 10.1093/bioinformatics/btab493 | ||||||||||||
Status: | Peer Reviewed | ||||||||||||
Publication Status: | Published | ||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
Date of first compliant deposit: | 4 January 2023 | ||||||||||||
Date of first compliant Open Access: | 4 January 2023 | ||||||||||||
RIOXX Funder/Project Grant: |
|
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year