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Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and
Bert Bogaerts1, Julien Van Braekel1, Alexander Van Uffelen1
1Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.
BMC Genomics
|January 8, 2025
Summary
Sciensano implemented a user-friendly Galaxy bioinformatics portal for whole genome sequencing (WGS) data analysis. This resource provides custom tools and pipelines for microbial pathogen characterization, aiding public health and diagnostics.
Area of Science:
- Bioinformatics
- Genomic Surveillance
- Public Health Microbiology
Background:
- Increasing whole genome sequencing (WGS) data presents bioinformatics analysis challenges in public health and clinical diagnostics.
- Laboratories often face bottlenecks due to a lack of bioinformatics expertise and accessible tools.
Purpose of the Study:
- To implement an intuitive and user-friendly bioinformatics tool portal using the Galaxy platform at Sciensano, the Belgian national public health institute.
- To provide a centralized resource for analyzing WGS data for microbial pathogen typing, characterization, and outbreak detection.
Main Methods:
- Development and implementation of a Galaxy instance (Galaxy @Sciensano) offering community tools and over 50 custom-developed pipelines.
- Creation of 'push-button' pipelines for automated analysis including quality control, de novo assembly, antimicrobial resistance prediction, and species-specific assays.
- Integration and regular synchronization with recognized databases like PubMLST, EnteroBase, and the NCBI National Database of Antibiotic Resistant Organisms.
Main Results:
- The Galaxy @Sciensano portal offers a wide range of tools focused on WGS data analysis for microbial pathogens.
- Custom pipelines provide complete characterization of bacterial isolates with interactive HTML reports.
- Tools are tailored for key pathogens (e.g., Escherichia coli, Listeria monocytogenes, Salmonella spp., Mycobacterium tuberculosis) and used in routine surveillance and ISO-accredited activities.
Conclusions:
- The Galaxy @Sciensano portal enhances bioinformatics capacity for public health laboratories by providing accessible and reproducible WGS data analysis tools.
- This resource supports reliable pathogen characterization and outbreak detection, crucial for effective public health interventions.
- The portal is publicly available for noncommercial use, promoting wider adoption of advanced genomic analysis in infectious disease surveillance.
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