cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20319094
title: Table S3 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319094.v1
title: Table S3 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319100.v1
title: Table S10 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319100
title: Table S10 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319106
title: Table S8 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319109
title: Table S1 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319109.v1
title: Table S1 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319106.v1
title: Table S8 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319112
title: Table S5 - S7 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319112.v1
title: Table S5 - S7 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319124
title: Table S9 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319124.v1
title: Table S9 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
DOI: 10.6084/m9.figshare.20319130
title: Table S2 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations

description: The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000 s of genomes to the species/subspecies and population levels for <i>Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio</i> and <i>Streptococcus</i>. 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 <i>Streptococcus.</i> HierCC was also consistent with legacy eBGs/ST Complexes in <i>Salmonella</i> or <i>Escherichia</i> and with O serogroups in <i>Salmonella</i>. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.