@article{52ffbbd2df7646cfae5fbd106d417c14,
title = "Swarm v3: Towards tera-scale amplicon clustering",
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.",
author = "Fr{\'e}d{\'e}ric Mah{\'e} and Lucas Czech and Alexandros Stamatakis and Christopher Quince and {de Vargas}, Colomban and Micah Dunthorn and Torbj{\o}rn Rognes",
note = "Acknowledgements: The authors thank {\'E}tienne Platini and Milena K{\"o}nigshoffen for writing unit tests, and Claude Monet for providing the impressionist background. The bioinformatics analyses were performed on the Core Cluster of the Institut Fran{\c c}ais de Bioinformatique (IFB) (ANR-11-INBS-0013). We are also grateful for access to computational resources provided by UNINETT Sigma2-the National Infrastructure for High Performance Computing and Data Storage in Norway (project NN9383K), the University of Oslo and the Oregon State University. Funding Information: This work was supported by the Gordon and Betty Moore Foundation through the UniEuk grant GBMF5275, the Klaus Tschira Foundation, and the Deutsche Forschungsgemeinschaft (#DU1319/5-1).",
year = "2022",
month = jan,
day = "1",
doi = "10.1093/bioinformatics/btab493",
language = "English",
volume = "38",
pages = "267--269",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "1",
}