Swarm v3: towards tera-scale amplicon clustering

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 https://github.com/torognes/swarmSupplementary information: Supplementary data are available at Bioinformatics online.

Mots clés

Open Source amplicon clustering operational taxonomic units

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Bio-informatique [q-bio.QM]

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btab493.pdf (171.09 Ko)

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https://hal.sorbonne-universite.fr/hal-03284105

Soumis le : lundi 12 juillet 2021-13:07:03

Dernière modification le : vendredi 12 avril 2024-15:28:03

Archivage à long terme le : mercredi 13 octobre 2021-18:53:12

Dates et versions

hal-03284105 , version 1 (12-07-2021)

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HAL Id : hal-03284105 , version 1
DOI : 10.1093/bioinformatics/btab493
WOS : 000736120000040

Citer

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

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