The SPSP—a national infrastructure for the storage and sharing of microbial genomic data in Switzerland—is broadening its scope to better support bacterial pathogen surveillance. While the platform has predominantly been used for viral data since the COVID-19 pandemic, there is now a strategic push to adapt it for more comprehensive bacterial genome analysis.
To that end, the IMMense pipeline—developed at the Institute for Medical Microbiology at UZH—will be extended and partially redesigned thanks to funding from Swissuniversities. This upgrade aims to accommodate a wider variety of bacterial species, emerging sequencing data types, and species-specific analyses. A key component of this initiative is the creation of an in silico reference dataset that will serve as a rigorous benchmark for validating the reproducibility and quality of IMMense’s analyses.
Moreover, the project will enhance SPSP’s frontend interface, improving scientists’ ability to explore and visualize the results generated by the IMMense pipeline—thereby boosting the platform’s usability and impact.
Why It Matters:
This extension reinforces SPSP’s commitment to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) and addresses the growing demand for standardized, high-quality bacterial genomic data in public health surveillance.
Explore the projet here.