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Swarm v3: Towards tera-scale amplicon clustering

Mahe F., Czech L., Stamatakis A., Quince C., de Vargas C., Dunthorn M., Rognes T.. 2022. Bioinformatics, 38 (1) : p. 267-269.

DOI: 10.1093/bioinformatics/btab493

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.

Mots-clés : logiciel; technique analytique; séquence d'adn; taxonomie; Échantillonnage; séquence répétée

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