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Data for The user’s guide to comparative genomics with EnteroBase
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Zhou, Zhemin, Alikhan, Nabil-Fareed, Mohamed, Khaled, Fan, Yulei and Achtman, Mark (2019) Data for The user’s guide to comparative genomics with EnteroBase. [Dataset]
![[img]](http://wrap.warwick.ac.uk/style/images/fileicons/application_vnd.ms-excel.png) |
Microsoft Excel (Detailed metadata for genomes of 328 Salmonella enterica serovar Agama HC2000|299 isolates)
Online Table 1.xlsx - Published Version Available under License Creative Commons Attribution 4.0. Download (72Kb) |
Official URL: https://wrap.warwick.ac.uk/128112
Abstract
EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera that include pathogens. Here we provide an overview on how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio, and Moraxella, and genotyped those assemblies by core genome Multilocus Sequence Typing (cgMLST). Hierarchical clustering of cgMLST sequence types has identified large numbers of populations at multiple levels of resolution, and a new bacterial strain can be mapped to those predefined population structures within a few hours after uploading its short reads. Case study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports SNP calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of Yersinia pestis over the last 5,000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3 which presents a novel, global overview of the population structure of all of the species, subspecies and clades within Escherichia.
| Item Type: | Dataset | |||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Type of Data: | Excel spreadsheet of Metadata | |||||||||
| Library of Congress Subject Headings (LCSH): | Comparative genomics, Salmonella -- Genetic aspects, Yersinia pestis , Escherichia | |||||||||
| Publisher: | University of Warwick, Warwick Medical School | |||||||||
| Official Date: | 18 October 2019 | |||||||||
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| Status: | Not Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Media of Output (format): | .xlsx | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Copyright Holders: | University of Warwick | |||||||||
| Description: | Detailed metadata for genomes of 328 Salmonella enterica serovar Agama HC2000|299 isolates. Comprises Online Table 1 of related publication. |
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| Date of first compliant deposit: | 18 October 2019 | |||||||||
| Date of first compliant Open Access: | 18 October 2019 | |||||||||
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