Year: 2021
Type: article
Abstract: 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.
Source: Bioinformatics
Institutions: Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institut de Recherche pour le Développement, Plant Health Institute de Montpellier, Carnegie Institution for Science, Carnegie Department of Plant Biology, Heidelberg Institute for Theoretical Studies, Karlsruhe Institute of Technology, Quadram Institute, University of Warwick, Earlham Institute, Centre National de la Recherche Scientifique, Station Biologique de Roscoff, Sorbonne Université, Adaptation et Diversité en Milieu Marin, University of Oslo, University of Duisburg-Essen, Oslo University Hospital
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,058
OpenAlex ID: W3182084436