Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection
Abstract The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an in...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11182-5 |
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| author | Bert Bogaerts Julien Van Braekel Alexander Van Uffelen Jolien D’aes Maxime Godfroid Thomas Delcourt Michael Kelchtermans Kato Milis Nathalie Goeders Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Raf Winand Kevin Vanneste |
| author_facet | Bert Bogaerts Julien Van Braekel Alexander Van Uffelen Jolien D’aes Maxime Godfroid Thomas Delcourt Michael Kelchtermans Kato Milis Nathalie Goeders Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Raf Winand Kevin Vanneste |
| author_sort | Bert Bogaerts |
| collection | DOAJ |
| description | Abstract The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive and user-friendly bioinformatics tool portal was implemented using Galaxy, an open-source platform for data analysis and workflow creation. The Galaxy @Sciensano instance is available to both internal and external scientists and offers a wide range of tools provided by the community, complemented by over 50 custom tools and pipelines developed in-house. The tool selection is currently focused primarily on the analysis of WGS data generated using Illumina sequencing for microbial pathogen typing, characterization and outbreak detection, but it also addresses specific use cases for other data types. Our Galaxy instance includes several custom-developed 'push-button' pipelines, which are user-friendly and intuitive stand-alone tools that perform complete characterization of bacterial isolates based on WGS data and generate interactive HTML output reports with key findings. These pipelines include quality control, de novo assembly, sequence typing, antimicrobial resistance prediction and several relevant species-specific assays. They are tailored for pathogens with active genomic surveillance programs, and clinical relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. and Mycobacterium tuberculosis. These tools and pipelines utilize internationally recognized databases such as PubMLST, EnteroBase, and the NCBI National Database of Antibiotic Resistant Organisms, which are automatically synchronized on a regular basis to ensure up-to-date results. Many of these pipelines are part of the routine activities of Belgian national reference centers and laboratories, some of which use them under ISO accreditation. This resource is publicly available for noncommercial use at https://galaxy.sciensano.be/ and can help other laboratories establish reliable, traceable and reproducible bioinformatics analyses for pathogens encountered in public health settings. |
| format | Article |
| id | doaj-art-0ad8e79a939e4af59fb9ec45f2d3bbd5 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-0ad8e79a939e4af59fb9ec45f2d3bbd52025-01-12T12:09:17ZengBMCBMC Genomics1471-21642025-01-0126112110.1186/s12864-024-11182-5Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detectionBert Bogaerts0Julien Van Braekel1Alexander Van Uffelen2Jolien D’aes3Maxime Godfroid4Thomas Delcourt5Michael Kelchtermans6Kato Milis7Nathalie Goeders8Sigrid C. J. De Keersmaecker9Nancy H. C. Roosens10Raf Winand11Kevin Vanneste12Transversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoTransversal Activities in Applied Genomics, SciensanoAbstract The influx of whole genome sequencing (WGS) data in the public health and clinical diagnostic sectors has created a need for data analysis methods and bioinformatics expertise, which can be a bottleneck for many laboratories. At Sciensano, the Belgian national public health institute, an intuitive and user-friendly bioinformatics tool portal was implemented using Galaxy, an open-source platform for data analysis and workflow creation. The Galaxy @Sciensano instance is available to both internal and external scientists and offers a wide range of tools provided by the community, complemented by over 50 custom tools and pipelines developed in-house. The tool selection is currently focused primarily on the analysis of WGS data generated using Illumina sequencing for microbial pathogen typing, characterization and outbreak detection, but it also addresses specific use cases for other data types. Our Galaxy instance includes several custom-developed 'push-button' pipelines, which are user-friendly and intuitive stand-alone tools that perform complete characterization of bacterial isolates based on WGS data and generate interactive HTML output reports with key findings. These pipelines include quality control, de novo assembly, sequence typing, antimicrobial resistance prediction and several relevant species-specific assays. They are tailored for pathogens with active genomic surveillance programs, and clinical relevance, such as Escherichia coli, Listeria monocytogenes, Salmonella spp. and Mycobacterium tuberculosis. These tools and pipelines utilize internationally recognized databases such as PubMLST, EnteroBase, and the NCBI National Database of Antibiotic Resistant Organisms, which are automatically synchronized on a regular basis to ensure up-to-date results. Many of these pipelines are part of the routine activities of Belgian national reference centers and laboratories, some of which use them under ISO accreditation. This resource is publicly available for noncommercial use at https://galaxy.sciensano.be/ and can help other laboratories establish reliable, traceable and reproducible bioinformatics analyses for pathogens encountered in public health settings.https://doi.org/10.1186/s12864-024-11182-5GalaxyPublic healthWhole genome sequencingGenomic surveillance |
| spellingShingle | Bert Bogaerts Julien Van Braekel Alexander Van Uffelen Jolien D’aes Maxime Godfroid Thomas Delcourt Michael Kelchtermans Kato Milis Nathalie Goeders Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Raf Winand Kevin Vanneste Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection BMC Genomics Galaxy Public health Whole genome sequencing Genomic surveillance |
| title | Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection |
| title_full | Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection |
| title_fullStr | Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection |
| title_full_unstemmed | Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection |
| title_short | Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection |
| title_sort | galaxy sciensano a comprehensive bioinformatics portal for genomics based microbial typing characterization and outbreak detection |
| topic | Galaxy Public health Whole genome sequencing Genomic surveillance |
| url | https://doi.org/10.1186/s12864-024-11182-5 |
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