HierCC: a multi-level clustering scheme for population assignments based on core genome MLST
Related Experiment Video
Updated: Nov 10, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Zhemin Zhou1, Jane Charlesworth1, Mark Achtman1
1Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
Motivation:
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.
Availability And Implementation:
https://enterobase.warwick.ac.uk/ and Source code and instructions: https://github.com/zheminzhou/pHierCC.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
More Related Videos
05:53Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
10:33Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis
Published on: June 17, 2019
Related Concept Videos
Modern Molecular Taxonomy
Cluster Sampling Method
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...
Applications of Molecular Taxonomy
Evolutionary Relationships through Genome Comparisons
DNA Microarrays
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...