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Nabil-Fareed Alikhan

MicroBinfie Podcast, 45 Software deep dive Enterobase

microbinfie, podcast1 min read

We chat with Nabil about EnteroBase, and learn about the background to the project, the general benefits of the platforms and some of the strange quirks users might encounter. EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Papers: Mentioned PLOS genetics paper: Alikhan et al. (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 14 (4): e1007261 https://doi.org/10.1371/journal.pgen.1007261 Paper describing Enterobase and the genome fishing expeditions: Zhou et al. (2020) The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity. Genome Res. 30:138-152. https://doi.org/10.1101/gr.251678.119 rMLST is described in: Jolley et al. 2012 Microbiology 158:1005-15. https://doi.org/10.1099/mic.0.055459-0 Resources Enterobase: http://enterobase.warwick.ac.uk/ PubMLST https://pubmlst.org/ About EnteroBase schemes: https://enterobase.readthedocs.io/en/latest/enterobase- tutorials/deeper-lineages.html Software: Enterobase toolkit and background software: https://github.com/zheminzhou/EToKi Errata. Jay Hinton’s Salmonella is a ST313 (D23580), not ST131 (I always mix the numbers up -- Nabil)