Swarm v3: Towards tera-scale amplicon clustering

Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)267-269
Number of pages3
JournalBioinformatics
Volume38
Issue number1
Early online date9 Jul 2021
DOIs
Publication statusPublished - 1 Jan 2022

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