A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens

This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens...

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Bibliographic Details
Published inMethods in molecular biology (Clifton, N.J.) Vol. 2852; p. 199
Main Authors Timme, Ruth E, Pfefer, Tina, Bias, C Hope, Allard, Marc W, Huang, Xinyang, Strain, Errol, Balkey, Maria
Format Journal Article
LanguageEnglish
Published United States 2025
Subjects
Data Curation - methods
Databases, Genetic
Genome, Bacterial
Genomics - methods
Genomics - standards
Humans
Quality Control
Software
Foodborne pathogens
WGS
GenomeTrakr
Surveillance
Pathogen genomic surveillance
Genomics
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Summary:This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens collected for different purposes. There are five protocols included in this chapter: (1) quality control (QC) assessment for the genome sequence data, (2) validation for the contextual data, (3) data submission for the standard pathogen package or Pathogen Data Object Model (DOM) to the public repository, (4) viewing and querying data at NCBI, and (5) data curation for maintaining relevance of public data. The data are available through one of the International Nucleotide Sequence Database Consortium (INSDC) members, with the National Center for Biotechnology Information (NCBI) being the primary focus of this document. NCBI Pathogen Detection is a custom dashboard at NCBI that provides easy access to pathogen data plus results for a standard suite of automated cluster and genotyping analyses important for informing public health and regulatory decision-making.
ISSN:1940-6029
DOI:10.1007/978-1-0716-4100-2_14