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. 2021 Dec 22;38(1):267-269.
doi: 10.1093/bioinformatics/btab493.

Swarm v3: towards tera-scale amplicon clustering

Frédéric Mahé  1   2 , Lucas Czech  3   4 , Alexandros Stamatakis  3   5 , Christopher Quince  6   7   8 , Colomban de Vargas  9   10 , Micah Dunthorn  11   12 , Torbjørn Rognes  13   14
Affiliations

Swarm v3: towards tera-scale amplicon clustering

Frédéric Mahé et al. Bioinformatics. .

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.

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