Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
1
Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, maryland, United states
2
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States
3
Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
4
Food Safety and Inspection Service, US Department of Agriculture, Athens, Georgia, United States
5
Food Safety and Inspection Service, US Department of Agriculture, Wahington, DC, United States
6
Center for Food Safety, University of Georgia, Griffin, Georgia, United States
- Published
- Accepted
- Subject Areas
- Bioinformatics, Evolutionary Studies, Food Science and Technology, Genomics, Epidemiology
- Keywords
- benchmark datasets, phylogenomics, food safety, foodborne outbreak, Salmonella, Listeria, E.coli, validation, WGS
- Copyright
- © 2017 Timme et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ Preprints 5:e3107v1 https://doi.org/10.7287/peerj.preprints.3107v1
Abstract
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Listeria monocytogenes stone fruit food recall dataset
This standard dataset table can be used for easy download of linked data using the Gen-FS Gopher script described in this manuscript.
Campylobacter jejuni raw milk outbreak dataset
This standard dataset table can be used for easy download of linked data using the Gen-FS Gopher script described in this manuscript.
Escherichia coli sprouts outbreak dataset
This standard dataset table can be used for easy download of linked data using the Gen-FS Gopher script described in this manuscript.
Salmonella enterica epi-validated outbreak dataset
This standard dataset table can be used for easy download of linked data using the Gen-FS Gopher script described in this manuscript.
Simulated outbreak from known phylogeny and reference genome
This standard dataset table can be used for easy download of linked data using the Gen-FS Gopher script described in this manuscript.