HierCC: a multi-level clustering scheme for population assignments based on core genome MLST.
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- Record sourced from PubMed, PMID 33823553.
- Also identified by DOI 10.1093/bioinformatics/btab234 and PMC identifier 8545296.
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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. https://enterobase.warwick.ac.uk/ and Source code and instructions: https://github.com/zheminzhou/pHierCC. Supplementary data are available at Bioinformatics online.