EnteroBase

A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Enteric Bacteria

EnteroBase aims to establish a world-class, one-stop, user-friendly, backwards-compatible but forward-looking genome database, Enterobase – together with a set of web-based tools, EnteroBase Backend Pipeline – to enable bacteriologists to identify, analyse, quantify and visualize genomic variation principally within the genera:

EnteroBase is populated with over 200,000 of genomic assemblies derived from publicly available complete genomes, sequence read archives and user uploads. Click here to Post an issue or bug about EnteroBase

Funded by BBSRC research grant BB/L020319/1.

Citation

If you use data/metadata from the website, or the analysis based on these data, please cite EnteroBase as:

Alikhan NF, Zhou Z,Sergeant MJ, Achtman M (2018) “A genomic overview of the population structure of Salmonella.” PLoS Genet 14 (4): e1007261. https://doi.org/10.1371/journal.pgen.1007261

If you use GrapeTree please cite:

Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carrico JA, Achtman M (2018) “GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens”, Genome Research; https://doi.org/10.1101/gr.232397.117

3rd Party acknowledgements

If you use data generated by 3rd party tools in EnteroBase, please cite both EnteroBase and the paper describing the specific tool.

Beghain J, Bridier-Nahmias A, Le NH, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb.Genom. 2018; 4 (7); https://dx.doi.org/10.1099/mgen.0.000192
  • EzClermont is described in:
Waters N, Brennan F, Holmes A, Abram F, Pritchard L. Easily phylotyping E. coli via the EzClermont web app and command-line tool. BioRxiv 2018; 317610; https://doi.org/10.1101/317610
  • FimTyper is described in:
Roer L, Tchesnokova V, Allesoe R, Muradova M, Chattopadhyay S, Ahrenfeldt J, Thomsen MCF, Lund O, Hansen F, Hammerum AM, Sokurenko E, Hasman H. Development of a web tool for Escherichia coli subtyping based on fimH alleles. J.Clin.Microbiol. 2017; 55 (8):2538-2543; https://doi.org/10.1128/JCM.00737-17

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