RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Xiaoming Xu
- Zekun Yin
- Lifeng Yan
- Huiguang Yi
- Hua Wang
- Bertil Schmidt
- Weiguo Liu
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:001189254800007&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/bioinformatics/btad695
- eISSN
- 1367-4811
- Externe Identifier
- Clarivate Analytics Document Solution ID: LU2S4
- PubMed Identifier: 37971961
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 11
- Zeitschrift
- BIOINFORMATICS
- Artikelnummer
- ARTN btad695
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Titel
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
- Sub types
- Article
- Ausgabe der Zeitschrift
- 39
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Abstract
- <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.</jats:p> </jats:sec>
- Autoren
- Xiaoming Xu
- Zekun Yin
- Lifeng Yan
- Huiguang Yi
- Hua Wang
- Bertil Schmidt
- Weiguo Liu
- DOI
- 10.1093/bioinformatics/btad695
- Editoren
- Tobias Marschall
- eISSN
- 1367-4811
- Ausgabe der Veröffentlichung
- 11
- Zeitschrift
- Bioinformatics
- Sprache
- en
- Online publication date
- 2023
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/bioinformatics/btad695
- Datum der Datenerfassung
- 2023
- Titel
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
- Ausgabe der Zeitschrift
- 39
Data source: Crossref
- Abstract
- <h4>Summary</h4>We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation.<h4>Availability and implementation</h4>RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.
- Addresses
- School of Software, Shandong University, Jinan, China.
- Autoren
- Xiaoming Xu
- Zekun Yin
- Lifeng Yan
- Huiguang Yi
- Hua Wang
- Bertil Schmidt
- Weiguo Liu
- DOI
- 10.1093/bioinformatics/btad695
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Identifier: 37971961
- PubMed Central ID: PMC10681859
- Funding acknowledgements
- NSFC: 61972231
- Engineering Research Center of Digital Media Technology, Ministry of Education, China:
- NSFC: 62102231
- Open access
- true
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 11
- Zeitschrift
- Bioinformatics (Oxford, England)
- Schlüsselwörter
- Genome, Bacterial
- Software
- Biological Evolution
- Sprache
- eng
- Medium
- Open access status
- Open Access
- Paginierung
- btad695
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2023
- Titel
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.
- Sub types
- brief-report
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 39
Files
https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad695/53474281/btad695.pdf https://europepmc.org/articles/PMC10681859?pdf=render
Data source: Europe PubMed Central
- Abstract
- SUMMARY: We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation. AVAILABILITY AND IMPLEMENTATION: RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.
- Date of acceptance
- 2023
- Autoren
- Xiaoming Xu
- Zekun Yin
- Lifeng Yan
- Huiguang Yi
- Hua Wang
- Bertil Schmidt
- Weiguo Liu
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/37971961
- DOI
- 10.1093/bioinformatics/btad695
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Central ID: PMC10681859
- Funding acknowledgements
- NSFC: 61972231
- Engineering Research Center of Digital Media Technology, Ministry of Education, China:
- Ausgabe der Veröffentlichung
- 11
- Zeitschrift
- Bioinformatics
- Schlüsselwörter
- Genome, Bacterial
- Software
- Biological Evolution
- Sprache
- eng
- Country
- England
- PII
- 7424710
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2023
- Titel
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 39
Data source: PubMed
- Autoren
- Xiaoming Xu
- Zekun Yin
- Lifeng Yan
- Huiguang Yi
- Hua Wang
- Bertil Schmidt
- Weiguo Liu
- Zeitschrift
- Bioinform.
- Artikelnummer
- 10
- Datum der Veröffentlichung
- 2023
- Titel
- RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.
- Ausgabe der Zeitschrift
- 39
Data source: DBLP
- Beziehungen:
- Property of