Project description

The Swiss Pathogen Surveillance Platform (SPSP) is an infrastructure to store and share genomic data from microbes and is seen as positive example across Europe. Labs, data scientists, authorities and federal offices heavily use SPSP since the COVID-19 pandemic, especially for viruses. The objective of this project is to extend SPSP for bacterial genome sequences. IMMense is the analysis pipeline processing bacterial sequencing data within SPSP and is being developed as an open-source data analysis pipeline at the Institute for Medical Microbiology at UZH. With a steadily growing number of bacterial species being added to SPSP, new sequencing data types becoming relevant and species- specific analyses being requested, IMMense has to be extended and partly redesigned to fullfill all the needs. Reproducibility of analyses within such a clinically relevant pipeline is critital. Therefore all updates and feature additions require careful quality control (QC) and validation. For this, a validated in-silico reference dataset of all relevant species could be used.

SPSP can currently store bacterial data and share it with other repositories and authorities but there is limited frontend capabilities allowing scientists to explore the data generated by IMMense which limits SPSP’s usefulness.

In this project, we plan to extend IMMense to cover the current top priority analyses needed for SPSP, generate a reference dataset to regularly benchmark the quality of the output of IMMense, and develop additional frontend capabilities to visualize the results generated by IMMense.

Funding source

Swissuniversities Call B3.2: ORD Funding for Existing Research Infrastructures of Strategic Relevance