Swarm v3: towards tera-scale amplicon clustering

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...

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Detalles Bibliográficos
Autores principales: Mahé, Frédéric, Czech, Lucas, Stamatakis, Alexandros, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, Rognes, Torbjørn
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696092/
https://www.ncbi.nlm.nih.gov/pubmed/34244702
http://dx.doi.org/10.1093/bioinformatics/btab493
Descripción
Sumario: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. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are available at https://github.com/torognes/swarm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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