Swarm v3: towards tera-scale amplicon clustering

• DOI: 10.1093/bioinformatics/btab493
• Publication Date: 2021-07-01T12:30:15Z
• Authors: Frédéric Mahé; Lucas Czech; Alexandros Stamat...; Christopher Quince; Colomban de Vargas; Micah Dunthorn; Torbjørn Rognes
• Keywords: ddc:004; 0301 basic medicine; 570; taxonomie; logiciel; http://aims.fao.org/aos/agrovoc/c_24008; http://aims.fao.org/aos/agrovoc/c_27812; operational taxonomic units; F30 - Génétique et amélioration des plantes; http://aims.fao.org/aos/agrovoc/c_6774; 03 medical and health sciences; Cluster Analysis; Open Source; U10 - Informatique, mathématiques et statistiques; DATA processing & computer science; http://aims.fao.org/aos/agrovoc/c_1513; amplicon clustering; séquence d'adn; échantillonnage; Applications Notes; 004; technique analytique; http://aims.fao.org/aos/agrovoc/c_f0eb96ed; séquence répétée; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; Biologie; info:eu-repo/classification/ddc/004; http://aims.fao.org/aos/agrovoc/c_7631; Software

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.