We will introduce bioinformatics approaches for the analysis, surveillance and phenotypic assessment of SARS-CoV-2 and its variants of concern (VOC). This will involve approaches for SARS-CoV-2 genome reconstruction from raw sequencing data (Illumina, ONT), lineage assignment, genomic profiling and phenotypic inference, clustering of sequences, phylogeny and genome-based incidence estimation.
The students will work hands-on with real data and conduct small projects, which will be presented on week 2. A typical day in week one will consist of lectures highlighting the biological-, public health and methodological background, hands-on work followed by short concluding summaries. Towards the end of the day, the students will work in-depth on their designated projects that will be presented in week 2.