Swarm v3: towards tera-scale amplicon clustering

被引：68

作者：

Mahe, Frederic ^{[1
,2
]}

Czech, Lucas ^{[3
,4
]}

Stamatakis, Alexandros ^{[3
,5
]}

Quince, Christopher ^{[6
,7
,8
]}

de Vargas, Colomban ^{[9
,10
]}

Dunthorn, Micah ^{[11
,12
]}

Rognes, Torbjorn ^{[13
,14
]}

机构：

[1] CIRAD, UMR PHIM, Montpellier, France

[2] Univ Montpellier, PHIM Plant Hlth Inst, Inst Agro, INRAE,IRD,CIRAD, Montpellier, France

[3] Heidelberg Inst Theoret Studies, Computat Mol Evolut Grp, Heidelberg, Germany

[4] Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA

[5] Karlsruhe Inst Technol, Inst Theoret Informat, Karlsruhe, Germany

[6] Earlham Inst, Organisms & Ecosyst, Norwich, Norfolk, England

[7] Quadram Inst, Gut Microbes & Hlth, Norwich, Norfolk, England

[8] Univ Warwick, Warwick Med Sch, Coventry, W Midlands, England

[9] Sorbonne Univ, ECOMAP, UMR7144, Stn Biol Roscoff,CNRS, Roscoff, France

[10] Res Federat Study Global Ocean Syst Ecol & Evolut, FR2022 Tara GOSEE, Paris, France

[11] Univ Oslo, Nat Hist Museum, Oslo, Norway

[12] Univ Duisburg Essen, Eukaryot Microbiol, Essen, Germany

[13] Univ Oslo, Dept Informat, Oslo, Norway

[14] Oslo Univ Hosp, Rikshosp, Dept Microbiol, Oslo, Norway

来源：

BIOINFORMATICS | 2022年 / 38卷 / 01期

基金：

英国生物技术与生命科学研究理事会;

关键词：

D O I：

10.1093/bioinformatics/btab493

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：267 / 269

页数：3

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