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Swarm v3: towards tera-scale amplicon clustering

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. Availability: Source code and binaries are available at Supplementary information: Supplementary data are available at Bioinformatics online.
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Submitted on : Monday, July 12, 2021 - 1:07:03 PM
Last modification on : Wednesday, July 6, 2022 - 9:27:55 AM
Long-term archiving on: : Wednesday, October 13, 2021 - 6:53:12 PM


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Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, et al.. Swarm v3: towards tera-scale amplicon clustering. Bioinformatics, Oxford University Press (OUP), 2022, 38 (1), pp.267-269. ⟨10.1093/bioinformatics/btab493⟩. ⟨hal-03284105⟩



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