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Ag Data Commons migration begins October 18, 2023

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Data Extent

Data from: Use of long-read sequencing simulators to assess real-world applications for food safety

Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes are responsible for severe foodborne illnesses in the United States. Current identification methods require at least four days to identify STEC and six days for L. monocytogenes. Adoption of long-read, whole genome sequencing for testing could significantly reduce the time needed for identification, but method development costs are high. Therefore, the goal of this project was to use NanoSim-H software to simulate Oxford Nanopore sequencing reads to assess the feasibility of sequencing-based foodborne pathogen detection and guide experimental design. Sequencing reads were simulated for STEC, L. monocytogenes, and a 1:1 combination of STEC and Bos taurus genomes using NanoSim-H. This dataset includes all of the simulated reads generated by the project in fasta format. This dataset can be analyzed bioinformatically or used to test bioinformatic pipelines.

Release Date
Spatial / Geographical Coverage Area
POINT (-795.18665313721 40.077810523208)
Ag Data Commons
Spatial / Geographical Coverage Location
600 E Mermaid Ln, Wyndmoor, PA 19038
Temporal Coverage
November 1, 2021 to June 30, 2022
Contact Name
Counihan, Katrina
Contact Email
Public Access Level
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service