High throughput microbial whole genome sequencing and bioinformatics
The Microbial Genomics group, co-led by Helena Seth-Smith and Tim Roloff Handschin, provides end to end whole genome sequencing and computational analysis of microbial pathogens and other bacteria of interest. We support clinical diagnostics and pathogen tracking in hospitals, detailed custom analysis for national reference labs, high throughput genome sequencing for research groups, and public health surveillance with robust, reproducible genomic workflows.
Sharing of genomic data withing Switzerland and across the globe is essential for effective epidemiology. The Microbial Genomics group contributes to groups and networks such as
- the Swiss Pathogen Surveillance Platform (SPSP),
- the Pathogen Data Network (PDN) led by SIB, and
- the miGenomeSurv network in the DACH region.
We develop the nextflow pipeline IMMense to analyze microbial genomes. By contributing genomes and helping to set data and analysis standards the group helps to provide FAIR data to the scientific community.
We are constantly extending our bioinformatic toolbox to analyze difficult to study microbes and materials.