Swarm v3: towards tera-scale amplicon clustering Article Swipe
Frédéric Mahé
,
Lucas Czech
,
Alexandros Stamatakis
,
Christopher Quince
,
Colomban de Vargas
,
Micah Dunthorn
,
Torbjørn Rognes
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btab493
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btab493
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.
Related Topics
Concepts
Swarm behaviour
Tera-
Computer science
Cluster analysis
Source code
Scalability
Robustness (evolution)
Multithreading
Open source
Data mining
Parallel computing
Amplicon
Blacklist
Software
Artificial intelligence
Thread (computing)
Database
Operating system
Biology
World Wide Web
Gene
Biochemistry
Polymerase chain reaction
Metadata
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btab493
- https://academic.oup.com/bioinformatics/article-pdf/38/1/267/41891209/btab493.pdf
- OA Status
- hybrid
- Cited By
- 114
- References
- 21
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3182084436
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3182084436Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btab493Digital Object Identifier
- Title
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Swarm v3: towards tera-scale amplicon clusteringWork title
- Type
-
articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
-
2021-07-01Full publication date if available
- Authors
-
Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn RognesList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btab493Publisher landing page
- PDF URL
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https://academic.oup.com/bioinformatics/article-pdf/38/1/267/41891209/btab493.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/article-pdf/38/1/267/41891209/btab493.pdfDirect OA link when available
- Concepts
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Swarm behaviour, Tera-, Computer science, Cluster analysis, Source code, Scalability, Robustness (evolution), Multithreading, Open source, Data mining, Parallel computing, Amplicon, Blacklist, Software, Artificial intelligence, Thread (computing), Database, Operating system, Biology, World Wide Web, Gene, Biochemistry, Polymerase chain reactionTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
114Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 37, 2024: 31, 2023: 26, 2022: 15, 2021: 4Per-year citation counts (last 5 years)
- References (count)
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21Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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