Skip to main content
U.S. flag

An official website of the United States government

This site is currently in beta, and your feedback is helping shape its ongoing development.

Return to search results

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

Published by Agricultural Research Service | Department of Agriculture | Metadata Last Checked: January 27, 2026 | Last Modified: 2025-11-21
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.

Resources

57 resources available

Find Related Datasets

Click any tag below to search for similar datasets

Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
                                            [
  "005:18"
]
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>
distribution 
                                            [
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_10read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772694"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_50read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772697"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_75read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772700"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_100read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772703"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_250read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772706"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_500read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772709"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_750read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772712"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_1000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772715"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_2500read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772718"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_5000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772721"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_7500read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772724"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_10000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772727"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_50000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772730"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_75000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772736"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_100000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772739"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_250000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772784"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_500000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772793"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_10reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772814"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_50reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772817"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_75reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772820"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_100reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772823"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_250reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772826"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_500reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772829"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_750reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772832"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_1000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772835"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_2500reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772838"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_5000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772841"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_7500reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772844"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_10000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772847"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_50000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43772853"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_75000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773156"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_100000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773159"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_250000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773165"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_500000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773171"
  },
  {
    "@type": "dcat:Distribution",
    "title": "10 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773183"
  },
  {
    "@type": "dcat:Distribution",
    "title": "50 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773186"
  },
  {
    "@type": "dcat:Distribution",
    "title": "75 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773189"
  },
  {
    "@type": "dcat:Distribution",
    "title": "100 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773192"
  },
  {
    "@type": "dcat:Distribution",
    "title": "250 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773195"
  },
  {
    "@type": "dcat:Distribution",
    "title": "500 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773198"
  },
  {
    "@type": "dcat:Distribution",
    "title": "750 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773201"
  },
  {
    "@type": "dcat:Distribution",
    "title": "1000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773204"
  },
  {
    "@type": "dcat:Distribution",
    "title": "2500 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773207"
  },
  {
    "@type": "dcat:Distribution",
    "title": "5000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773210"
  },
  {
    "@type": "dcat:Distribution",
    "title": "7500 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773213"
  },
  {
    "@type": "dcat:Distribution",
    "title": "10000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773225"
  },
  {
    "@type": "dcat:Distribution",
    "title": "50000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773234"
  },
  {
    "@type": "dcat:Distribution",
    "title": "75000 Reads.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773243"
  },
  {
    "@type": "dcat:Distribution",
    "title": "100000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773261"
  },
  {
    "@type": "dcat:Distribution",
    "title": "250000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773276"
  },
  {
    "@type": "dcat:Distribution",
    "title": "500000 simulated.fasta",
    "format": "fasta",
    "mediaType": "text/plain",
    "downloadURL": "https://ndownloader.figshare.com/files/43773294"
  },
  {
    "@type": "dcat:Distribution",
    "title": "750000 simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/43773315"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_750000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/44730022"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_750000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/44730025"
  },
  {
    "@type": "dcat:Distribution",
    "title": "O157H7_1000000read_simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/44730058"
  },
  {
    "@type": "dcat:Distribution",
    "title": "Lmono_1000000reads_simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/44730061"
  },
  {
    "@type": "dcat:Distribution",
    "title": "1000000 simulated.fasta",
    "format": "fasta",
    "mediaType": "application/zip",
    "downloadURL": "https://ndownloader.figshare.com/files/44730067"
  }
]
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

data.gov

An official website of the GSA's Technology Transformation Services

Looking for U.S. government information and services?
Visit USA.gov