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HierCC : a multi-level clustering scheme for population assignments based on core genome MLST
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Zhou, Zhemin, Charlesworth, Jane, Achtman, Mark and Kelso, Janet (2021) HierCC : a multi-level clustering scheme for population assignments based on core genome MLST. Bioinformatics, 37 (20). pp. 3645-3646. doi:10.1093/bioinformatics/btab234 ISSN 1367-4803.
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WRAP-HierCC-multi-level-clustering-population-assignments-core-genome-2021.pdf - Accepted Version - Requires a PDF viewer. Download (1632Kb) | Preview |
Official URL: http://dx.doi.org/10.1093/bioinformatics/btab234
Abstract
Routine infectious disease surveillance is increasingly based on large-scale whole genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present pHierCC, a pipeline that defines a scalable clustering scheme, HierCC, based on core genome multi-locus typing that allows incremental, static, multi-level cluster assignments of genomes. We also present HCCeval, which identifies optimal thresholds for assigning genomes to cohesive HierCC clusters. HierCC was implemented in EnteroBase in 2018, and has since genotyped >530,000 genomes from Salmonella, Escherichia/Shigella, Streptococcus, Clostridioides, Vibrio and Yersinia.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||||||
Library of Congress Subject Headings (LCSH): | Genomes, Nucleotide sequence -- Databases, Communicable diseases, Cluster analysis -- Computer programs | ||||||||
Journal or Publication Title: | Bioinformatics | ||||||||
Publisher: | Oxford University Press | ||||||||
ISSN: | 1367-4803 | ||||||||
Official Date: | December 2021 | ||||||||
Dates: |
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Volume: | 37 | ||||||||
Number: | 20 | ||||||||
Page Range: | pp. 3645-3646 | ||||||||
DOI: | 10.1093/bioinformatics/btab234 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Reuse Statement (publisher, data, author rights): | This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Zhemin Zhou, Jane Charlesworth, Mark Achtman, HierCC: A multi-level clustering scheme for population assignments based on core genome MLST, Bioinformatics, 2021;, btab234, is available online at: https://doi.org/10.1093/bioinformatics/btab234 | ||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||
Date of first compliant deposit: | 12 April 2021 | ||||||||
Date of first compliant Open Access: | 6 April 2022 | ||||||||
RIOXX Funder/Project Grant: |
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