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Solu : a cloud platform for real-time genomic pathogen surveillance

Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega Sanz (UGent) , Jacob L. Steenwyk and Samuel Sihvonen
(2025) BMC BIOINFORMATICS. 26(1).
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Abstract
BackgroundGenomic 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.ResultsWe present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system.EvaluationSolu'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.ConclusionsBy 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.
Keywords
Workflow, Genomics, Whole-genome sequencing, Infection prevention, Outbreak, Phylogeny, Privacy, TOOL

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MLA
Saratto, Timo, et al. “Solu : A Cloud Platform for Real-Time Genomic Pathogen Surveillance.” BMC BIOINFORMATICS, vol. 26, no. 1, 2025, doi:10.1186/s12859-024-06005-z.
APA
Saratto, T., Visuri, K., Lehtinen, J., Ortega Sanz, I., Steenwyk, J. L., & Sihvonen, S. (2025). Solu : a cloud platform for real-time genomic pathogen surveillance. BMC BIOINFORMATICS, 26(1). https://doi.org/10.1186/s12859-024-06005-z
Chicago author-date
Saratto, Timo, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega Sanz, Jacob L. Steenwyk, and Samuel Sihvonen. 2025. “Solu : A Cloud Platform for Real-Time Genomic Pathogen Surveillance.” BMC BIOINFORMATICS 26 (1). https://doi.org/10.1186/s12859-024-06005-z.
Chicago author-date (all authors)
Saratto, Timo, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega Sanz, Jacob L. Steenwyk, and Samuel Sihvonen. 2025. “Solu : A Cloud Platform for Real-Time Genomic Pathogen Surveillance.” BMC BIOINFORMATICS 26 (1). doi:10.1186/s12859-024-06005-z.
Vancouver
1.
Saratto T, Visuri K, Lehtinen J, Ortega Sanz I, Steenwyk JL, Sihvonen S. Solu : a cloud platform for real-time genomic pathogen surveillance. BMC BIOINFORMATICS. 2025;26(1).
IEEE
[1]
T. Saratto, K. Visuri, J. Lehtinen, I. Ortega Sanz, J. L. Steenwyk, and S. Sihvonen, “Solu : a cloud platform for real-time genomic pathogen surveillance,” BMC BIOINFORMATICS, vol. 26, no. 1, 2025.
@article{01JHJE4C2PGQJGW9S8VHH5Q9WT,
  abstract     = {{BackgroundGenomic 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.ResultsWe present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system.EvaluationSolu'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.ConclusionsBy 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.}},
  articleno    = {{12}},
  author       = {{Saratto, Timo and Visuri, Kerkko and Lehtinen, Jonatan and Ortega Sanz, Irene and Steenwyk, Jacob L. and Sihvonen, Samuel}},
  issn         = {{1471-2105}},
  journal      = {{BMC BIOINFORMATICS}},
  keywords     = {{Workflow,Genomics,Whole-genome sequencing,Infection prevention,Outbreak,Phylogeny,Privacy,TOOL}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{13}},
  title        = {{Solu : a cloud platform for real-time genomic pathogen surveillance}},
  url          = {{http://doi.org/10.1186/s12859-024-06005-z}},
  volume       = {{26}},
  year         = {{2025}},
}
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