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 visualise genomic variation principally within the genera:


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Funded by BBSRC research grant BB/L020319/1.


If you use data/metadata from the website, or the analysis based on these data, please cite EnteroBase as:
Zhou Z., Alikhan NF, Mohamed K, the Agama Study Group, Achtman M (2020), “The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity”, Genome Res. 2020. 30: 138-152, https://doi.org/10.1101/gr.251678.119
Please cite Salmonella database as:

Achtman M, Zhou Z, Alikhan NF, et al. (2020) “Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project”, Wellcome Open Research 5, 223, https://doi.org/10.12688/wellcomeopenres.16291.1


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

Please cite Clostridioides database as:
Frentrup M, Zhou Z, Steglich M, et al. (2020) “A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics”, Microb Genom. 6(8). doi: http://dx.doi.org/10.1099/mgen.0.000410
If you use GrapeTree please cite the following paper:
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. 28(9): 1395–1404, https://doi.org/10.1101/gr.232397.117
If you use Hierarchical Clustering please cite the following paper:
Zhou Z, Charlesworth J and Achtman M (2021) “HierCC: A multi-level clustering scheme for population assignments based on core genome MLST” Bioinformatics, Vol37, 20:3645–3646

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.

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