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

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: May 05, 2026 at 11:42 PM | Dataset Last Updated: November 21, 2025
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.

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "005:18"
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contactPoint 
{
  "fn": "Counihan, Katrina",
  "hasEmail": "mailto:katrina.counihan@usda.gov"
}
description <p>Shiga toxin-producing <em>Escherichia coli</em> (STEC) and <em>Listeria monocytogenes</em> 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 <em>L. monocytogenes</em>. 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, <em>L. monocytogenes</em>, and a 1:1 combination of STEC and <em>Bos taurus</em> 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. </p>
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identifier 10.15482/USDA.ADC/1529447
keyword 
[
  "ARS",
  "Escherichia coli O157:H7",
  "Listeria monocytogenes",
  "MinION",
  "NP108",
  "data.gov",
  "long-read sequencing",
  "sequencing simulation"
]
license https://www.usa.gov/publicdomain/label/1.0/
modified 2025-11-21
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
spatial 
"{"type": "Point", "coordinates": [-795.18665313721, 40.077810523208]}"
temporal 2021-11-01/2022-06-30
title Data from: Use of long-read sequencing simulators to assess real-world applications for food safety

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