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Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

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143 days ago
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance https://t.co/dbqqwOLWhM
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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.

DOI: 10.7287/peerj.preprints.3107v1/supp-1

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.

DOI: 10.7287/peerj.preprints.3107v1/supp-2

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.

DOI: 10.7287/peerj.preprints.3107v1/supp-3

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.

DOI: 10.7287/peerj.preprints.3107v1/supp-4

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.

DOI: 10.7287/peerj.preprints.3107v1/supp-5

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ruth E Timme conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Hugh Rand conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Martin Shumway contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Eija K Trees contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Mustafa Simmons contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Richa Agarwala contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Steven Davis contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Glen Tillman contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Stephanie Defibaugh-Chavez contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Heather A Carleton contributed reagents/materials/analysis tools, reviewed drafts of the paper.

William A Klimke contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Lee S Katz conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

NCBI accessions (SRA, Biosample, Assembly, etc.) provided in Supplemental files.

Data Deposition

The following information was supplied regarding data availability:

GitHub

https://github.com/WGS-standards-and-analysis/datasets

Funding

This work was supported by the Center for Food Safety and Applied Nutrition at the Food and Drug Administration; the Advanced Molecular Detection (AMD) Initiative at Centers for Disease Control and Prevention; the Intramural Research Program of the National Institutes of Health, Library of Medicine; and USDA-FSIS program funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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