Solu: a cloud platform for real-time genomic pathogen surveillance
Abstract Background Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continu...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-06005-z |
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| author | Timo Saratto Kerkko Visuri Jonatan Lehtinen Irene Ortega-Sanz Jacob L. Steenwyk Samuel Sihvonen |
| author_facet | Timo Saratto Kerkko Visuri Jonatan Lehtinen Irene Ortega-Sanz Jacob L. Steenwyk Samuel Sihvonen |
| author_sort | Timo Saratto |
| collection | DOAJ |
| description | Abstract Background Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. The existing pipelines often require the user to set up and manage their own infrastructure and are not designed for continuous surveillance that demands integration of new and regularly generated sequencing data with previous analyses. Additionally, academic projects often do not meet the privacy requirements of healthcare providers. Results We present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system. Evaluation Solu’s accuracy for taxonomy assignment, antimicrobial resistance genes, and phylogenetics was comparable to established pathogen surveillance pipelines. In some cases, Solu identified antimicrobial resistance genes that were previously undetected. Together, these findings demonstrate the efficacy of our platform. Conclusions By enabling reliable, user-friendly, and privacy-focused genomic surveillance, Solu has the potential to bridge the gap between cutting-edge research and practical, widespread application in healthcare settings. The platform is available for free academic use at https://platform.solugenomics.com . |
| format | Article |
| id | doaj-art-f90c3d752a20496297d8818501d45a61 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-f90c3d752a20496297d8818501d45a612025-01-19T12:40:57ZengBMCBMC Bioinformatics1471-21052025-01-0126111310.1186/s12859-024-06005-zSolu: a cloud platform for real-time genomic pathogen surveillanceTimo Saratto0Kerkko Visuri1Jonatan Lehtinen2Irene Ortega-Sanz3Jacob L. Steenwyk4Samuel Sihvonen5Solu Healthcare OySolu Healthcare OySolu Healthcare OyDepartment of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent UniversityHowards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of CaliforniaSolu Healthcare OyAbstract Background Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. The existing pipelines often require the user to set up and manage their own infrastructure and are not designed for continuous surveillance that demands integration of new and regularly generated sequencing data with previous analyses. Additionally, academic projects often do not meet the privacy requirements of healthcare providers. Results We present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system. Evaluation Solu’s accuracy for taxonomy assignment, antimicrobial resistance genes, and phylogenetics was comparable to established pathogen surveillance pipelines. In some cases, Solu identified antimicrobial resistance genes that were previously undetected. Together, these findings demonstrate the efficacy of our platform. Conclusions By enabling reliable, user-friendly, and privacy-focused genomic surveillance, Solu has the potential to bridge the gap between cutting-edge research and practical, widespread application in healthcare settings. The platform is available for free academic use at https://platform.solugenomics.com .https://doi.org/10.1186/s12859-024-06005-zWorkflowGenomicsWhole-genome sequencingInfection preventionOutbreakPhylogeny |
| spellingShingle | Timo Saratto Kerkko Visuri Jonatan Lehtinen Irene Ortega-Sanz Jacob L. Steenwyk Samuel Sihvonen Solu: a cloud platform for real-time genomic pathogen surveillance BMC Bioinformatics Workflow Genomics Whole-genome sequencing Infection prevention Outbreak Phylogeny |
| title | Solu: a cloud platform for real-time genomic pathogen surveillance |
| title_full | Solu: a cloud platform for real-time genomic pathogen surveillance |
| title_fullStr | Solu: a cloud platform for real-time genomic pathogen surveillance |
| title_full_unstemmed | Solu: a cloud platform for real-time genomic pathogen surveillance |
| title_short | Solu: a cloud platform for real-time genomic pathogen surveillance |
| title_sort | solu a cloud platform for real time genomic pathogen surveillance |
| topic | Workflow Genomics Whole-genome sequencing Infection prevention Outbreak Phylogeny |
| url | https://doi.org/10.1186/s12859-024-06005-z |
| work_keys_str_mv | AT timosaratto soluacloudplatformforrealtimegenomicpathogensurveillance AT kerkkovisuri soluacloudplatformforrealtimegenomicpathogensurveillance AT jonatanlehtinen soluacloudplatformforrealtimegenomicpathogensurveillance AT ireneortegasanz soluacloudplatformforrealtimegenomicpathogensurveillance AT jacoblsteenwyk soluacloudplatformforrealtimegenomicpathogensurveillance AT samuelsihvonen soluacloudplatformforrealtimegenomicpathogensurveillance |