Swarm v3: Towards tera-scale amplicon clustering

Mahe Frédéric, Czech Lucas, Stamatakis Alexandros, Quince Christopher, de Vargas Colomban, Dunthorn Micah, Rognes Torbjørn. 2022. Swarm v3: Towards tera-scale amplicon clustering. Bioinformatics, 38 (1) : 267-269.

Url - autres données associées : https://github.com/torognes/swarm

Résumé : 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 Agrovoc : logiciel, technique analytique, séquence d'adn, taxonomie, échantillonnage, séquence répétée

Classification Agris : U10 - Informatique, mathématiques et statistiques
F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 7 (2019-) - Hors champs stratégiques

Auteurs et affiliations

• Mahe Frédéric, CIRAD-BIOS-UMR PHIM (FRA) ORCID: 0000-0002-2808-0984 - auteur correspondant
• Czech Lucas, Heidelberg Institute for Theoretical Studies (DEU)
• Stamatakis Alexandros, Heidelberg Institute for Theoretical Studies (DEU)
• Quince Christopher, Earlham Institute (GBR)
• de Vargas Colomban, Université Paris-Sorbonne (FRA)
• Dunthorn Micah, Natural History Museum (NOR)
• Rognes Torbjørn, University of Oslo (NOR)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/600351/)

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