EnteroBase

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

Databases

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:

Misc

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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:
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

or

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.

Click one of the links below to read more: