EnteroBase¶
A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Enteric Bacteria
- Click here to get started (registering and logging in.)
- Click here to see the tutorials.
Gallery¶
GrapeTree of cgMLST (3,002 loci) from 1,082
Salmonella enterica serovar Agona genomes
in EnteroBase
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Core SNP phylogeny of ancient (red) and
modern genomes of Para C Lineage in
Salmonella eneterica
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Alikhan et al. 2018 | Zhou et al. 2018a |
Visualization of 3,902 legacy Salmonella
MLST STs from 99,722 genomic assemblies
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Zhou et al. 2018b |
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¶
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:
- 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
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.
- rMLST is Copyright 2010-2016, University of Oxford. rMLST is described in: Jolley et al. 2012 Microbiology 158:1005-15.
- Serovar predictions (SISTR) have been calculated using the pipeline developed by the SISTR team and is described in Yoshida et al. 2016 PLoS ONE 11(1): e0147101 and evaluated in Robertson et al. 2018 M Gen 4(2):e000151
- SeqSero2 is described in Zhang et al. 2019 Appl Environ Microbiol 85:e01746-19
- ClermonTyping is described in Beghain et al. 2018 M Gen 4(7): e000192
- EzClermont is described in: Waters et al. 2020 DOI 10.1099/acmi.0.000143
- FimTyper is described in: Roer et al. 2017 J Clin Microbiol 55(8):2538-2543
Click one of the links below to read more:
- About EnteroBase
- Frequently Asked Questions
- Enterobase Terms and Conditions
- How EnteroBase uses your personal data (GDPR)
- Getting Started - Registering and logging in
- EnteroBase tutorials and worked examples
- Presentations and Lectures about EnteroBase
- About schemes within EnteroBase (cg/wg/r/MLST)
- HierCC (Hierarchical Clustering of CgMLST)
- GrapeTree Documentation
- Key features in Enterobase
- Enterobase API Usage
- The internal structure of EnteroBase
- HierCC equivalents
- Precomputed species trees
- Documentation previously on mlst.warwick.ac.uk
- Developing EnteroBase (Developers only)
- Local EnteroBase’s documentation