Accessible viral metagenomics for public health and clinical domains with Jovian
Abstract The integration of next-generation sequencing into clinical diagnostics and surveillance initiatives is impeded by the lack of data analysis pipelines that align with privacy legislation and laboratory certification protocols. To address these challenges, we developed Jovian, an open-source...
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Nature Portfolio
2024-10-01
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| Online Access: | https://doi.org/10.1038/s41598-024-73785-y |
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| author | Dennis Schmitz Florian Zwagemaker Sam Nooij Thierry K. S. Janssens Jeroen Cremer Robert Verhagen Harry Vennema Annelies Kroneman Marion P. G. Koopmans Jeroen F. J. Laros Miranda de Graaf |
| author_facet | Dennis Schmitz Florian Zwagemaker Sam Nooij Thierry K. S. Janssens Jeroen Cremer Robert Verhagen Harry Vennema Annelies Kroneman Marion P. G. Koopmans Jeroen F. J. Laros Miranda de Graaf |
| author_sort | Dennis Schmitz |
| collection | DOAJ |
| description | Abstract The integration of next-generation sequencing into clinical diagnostics and surveillance initiatives is impeded by the lack of data analysis pipelines that align with privacy legislation and laboratory certification protocols. To address these challenges, we developed Jovian, an open-source, virus-focused, metagenomic analysis workflow for Illumina data. Jovian generates scaffolds enriched with pertinent annotations, including taxonomic classification, combined with metrics needed for quality assessment (coverage depth, average GC content, localization of open reading frames, minority single nucleotide polymorphisms), and incorporates host and disease metadata. Interactive web-based reports with an audit trail are generated. Jovian was employed on four systems, hosted by three institutes, utilizing grid-computers, a high-performance compute singular server, and a Windows10 laptop. All systems yielded identical results with matching MD5sums. Comparison with a commercial online reference tool using viral gastroenteritis samples confirmed the identification of the same pathogens. Jovian provides comparable results to a commercially available online reference tool and generates identical results at different institutes with different IT architectures, proving it is portable and reproducible. Jovian addresses bottlenecks in the deployment of metagenomics within public health and clinical laboratories and has the potential to enhance the breadth of surveillance and testing programs, thereby fostering more effective public health interventions. |
| format | Article |
| id | doaj-art-5fb79f141aa4489e83833fac5a81c6ce |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-5fb79f141aa4489e83833fac5a81c6ce2025-08-20T02:18:35ZengNature PortfolioScientific Reports2045-23222024-10-0114111110.1038/s41598-024-73785-yAccessible viral metagenomics for public health and clinical domains with JovianDennis Schmitz0Florian Zwagemaker1Sam Nooij2Thierry K. S. Janssens3Jeroen Cremer4Robert Verhagen5Harry Vennema6Annelies Kroneman7Marion P. G. Koopmans8Jeroen F. J. Laros9Miranda de Graaf10National Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlNational Institute of Public Health and the Environment, Center for Infectious Disease ControlViroscience, Erasmus University Medical CenterDepartment of Bio-Informatics and Computational Services, National Institute of Public Health and the EnvironmentViroscience, Erasmus University Medical CenterAbstract The integration of next-generation sequencing into clinical diagnostics and surveillance initiatives is impeded by the lack of data analysis pipelines that align with privacy legislation and laboratory certification protocols. To address these challenges, we developed Jovian, an open-source, virus-focused, metagenomic analysis workflow for Illumina data. Jovian generates scaffolds enriched with pertinent annotations, including taxonomic classification, combined with metrics needed for quality assessment (coverage depth, average GC content, localization of open reading frames, minority single nucleotide polymorphisms), and incorporates host and disease metadata. Interactive web-based reports with an audit trail are generated. Jovian was employed on four systems, hosted by three institutes, utilizing grid-computers, a high-performance compute singular server, and a Windows10 laptop. All systems yielded identical results with matching MD5sums. Comparison with a commercial online reference tool using viral gastroenteritis samples confirmed the identification of the same pathogens. Jovian provides comparable results to a commercially available online reference tool and generates identical results at different institutes with different IT architectures, proving it is portable and reproducible. Jovian addresses bottlenecks in the deployment of metagenomics within public health and clinical laboratories and has the potential to enhance the breadth of surveillance and testing programs, thereby fostering more effective public health interventions.https://doi.org/10.1038/s41598-024-73785-yViromicsPublic healthClinicsDiagnosticsSurveillanceNext generation sequencing |
| spellingShingle | Dennis Schmitz Florian Zwagemaker Sam Nooij Thierry K. S. Janssens Jeroen Cremer Robert Verhagen Harry Vennema Annelies Kroneman Marion P. G. Koopmans Jeroen F. J. Laros Miranda de Graaf Accessible viral metagenomics for public health and clinical domains with Jovian Scientific Reports Viromics Public health Clinics Diagnostics Surveillance Next generation sequencing |
| title | Accessible viral metagenomics for public health and clinical domains with Jovian |
| title_full | Accessible viral metagenomics for public health and clinical domains with Jovian |
| title_fullStr | Accessible viral metagenomics for public health and clinical domains with Jovian |
| title_full_unstemmed | Accessible viral metagenomics for public health and clinical domains with Jovian |
| title_short | Accessible viral metagenomics for public health and clinical domains with Jovian |
| title_sort | accessible viral metagenomics for public health and clinical domains with jovian |
| topic | Viromics Public health Clinics Diagnostics Surveillance Next generation sequencing |
| url | https://doi.org/10.1038/s41598-024-73785-y |
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