ArticleFrontiers in microbiology2019
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center:
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- A WGS workflow for identifying genetically modified and foodborne-pathogenicFood chemistry. Molecular sciences · 2026Article
- 4CMenB vaccine coverage of invasive serogroup B meningococci collected in Belgium between 2016 and 2022.Human vaccines & immunotherapeutics · 2025Article
- MiST: rapid, accurate and flexible (core-genome) multi-locus sequence typing (MLST) allele calling from draft genomes.BMC genomics · 2025Article
- Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation ofJournal of clinical microbiology · 2025Article
- Formal verification of bioinformatics software using model checking and theorem proving.Briefings in bioinformatics · 2025Article
- Genomics for antimicrobial resistance-progress and future directions.Antimicrobial agents and chemotherapy · 2025Review
- Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection.BMC genomics · 2025Article
- Detection of antimicrobial resistance via state-of-the-art technologies versus conventional methods.Frontiers in microbiology · 2025Review
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- Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.Frontiers in microbiology · 2024Article
- Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae.Scientific reports · 2023Article
- Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards.Microbial genomics · 2023Article
- An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance.Nature communications · 2023Article
- Genomic insight intoFrontiers in veterinary science · 2023Article
- Article
- A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data.Microorganisms · 2022Article
- GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells.Nucleic acids research · 2022Article
- Outbreak of invasive meningococcal disease caused by a meningococcus serogroup B in a nursery school, Wallonia, Belgium, 2018.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2022Article
- Genomic insights ofFrontiers in microbiology · 2022Article
- Whole genome sequence analysis of Neisseria meningitidis strains circulating in Kazakhstan, 2017-2018.PloS one · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Despite being a well-established research method, the use of whole-genome sequencing (WGS) for routine molecular typing and pathogen characterization remains a substantial challenge due to the required bioinformatics resources and/or expertise. Moreover, many national reference laboratories and centers, as well as other laboratories working under a quality system, require extensive validation to demonstrate that employed methods are "fit-for-purpose" and provide high-quality results. A harmonized framework with guidelines for the validation of WGS workflows does currently, however, not exist yet, despite several recent case studies highlighting the urgent need thereof. We present a validation strategy focusing specifically on the exhaustive characterization of the bioinformatics analysis of a WGS workflow designed to replace conventionally employed molecular typing methods for microbial isolates in a representative small-scale laboratory, using the pathogen
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