@article {Zhou613554, author = {Zhemin Zhou and Nabil-Fareed Alikhan and Khaled Mohamed and the Agama Study Group and Mark Achtman}, editor = {Brown, Derek and Chattaway, Marie and Dallman, Tim and Delahay, Richard and Kornschober, Christian and Pietzka, Ariane and Malorny, Burkhard and Petrovska, Liljana and Robertson, Andy and Tyne, William and Fan, Yulei and Weill, Fran{\c c}ois-Xavier and Accou-Demartin, Marie and Williams, Nicola}, title = {The user{\textquoteright}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}, elocation-id = {613554}, year = {2019}, doi = {10.1101/613554}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 were assembled from short reads with SNP calls that were extracted from metagenomic sequences. Here we provide an overview for its users on how EnteroBase works, what it can do, and its future prospects. This user{\textquoteright}s guide is illustrated by three case studies ranging in scale from the miniscule (local transmission of Salmonella between neighboring social groups of badgers) through pandemic transmission of plague and microevolution of Yersinia pestis over the last 5,000 years to a novel, global overview of the population structure of all of Escherichia.}, URL = {https://www.biorxiv.org/content/early/2019/04/18/613554}, eprint = {https://www.biorxiv.org/content/early/2019/04/18/613554.full.pdf}, journal = {bioRxiv} }