Data for EnteroBase: Hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

Here we evaluate HierCC’s ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus.

HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated 36 identification of and assignment to species/subspecies and populations for multiple genera.<br><br>The full set of deposited files is listed below: Data Files: Cdiff.2021.HC5.cgMLST Cdiff.2021.HC5.cgMLST.alleles.fasta.gz Cdiff.2021.HC5.wgMLST_detail.presence.gz EscherichiaReps.cgMLST.alleles.fasta.gz EscherichiaReps.cgMLST EscherichiaReps.wgMLST_detail.presence.gz Salmonella.2021.HC5_lg4_OR_HC400.cgMLST Salmonella.2021.HC5_lg4_OR_HC400.cgMLST.alleles.fasta.gz Salmonella.2021.HC5_lg4_OR_HC400.wgMLST_detail.presence.gz Streptococcus.2021.HC5_lg4_OR_HC50.cgMLST Streptococcus.2021.HC5_lg4_OR_HC50.cgMLST.alleles.fasta.gz Streptococcus.2021.HC5_lg4_OR_HC50.wgMLST_detail.presence.gz Vibrio.2021.HC5.cgMLST Vibrio.2021.HC5.cgMLST.alleles.fasta.gz Vibrio.2021.HC5.wgMLST_detail.presence.gz Yersinia.2021.HC5.cgMLST Yersinia.2021.HC5.cgMLST.alleles.fasta.gz Yersinia.2021.HC5.wgMLST_detail.presence.gz For details, refer the Dataset (Zip), Readme and Metadata files