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The user’s guide to comparative genomics with EnteroBase. Three case studies: micro-clades within Salmonella enterica serovar Agama, ancient and modern populations of Yersinia pestis, and core genomic diversity of all Escherichia

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The user’s guide to comparative genomics with EnteroBase. Three case studies: micro-clades within Salmonella enterica serovar Agama, ancient and modern populations of Yersinia pestis, and core genomic diversity of all Escherichia
EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera including pathogens. It currently contains more than 300,000 genomes that have been assembled from Illumina short reads from the genera Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio , and Moraxella . With the recent introduction of hierarchical clustering of core genome MLST sequence types, EnteroBase now facilitates the identification of close relatives of bacteria within those genera inside of a few hours of uploading their short reads. It also supports private collaborations between groups of users, and the comparison of genomic data that...
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