Comparative Bacterial Genomics

The course will give an introduction to basic concepts and methodology in bacterial genomics. Topics will include handling of genomic sequencing raw data, i.e. assembly and annotation of bacterial genomes, as well as comparative genomic analysis (phylogenomics, typing methods, calculating pan- and core genomes) and functional genomic analysis (identifying toxin, virulence and antibiotic resistance genes) of bacterial genomes.

After completing the course, the student should be able to:
• demonstrate general knowledge of bacterial genomes and sequencing technologies,
• demonstrate knowledge of de novo assembly of bacterial genomes,
• perform quality control and annotation of bacterial genomes using bioinformatics tools,
• discuss general principles, suitability and limitations of sequence alignments at the nucleotide and protein level,
• use sequence alignments for phylogenomic analysis and in different typing methods,
• explain the concepts core and pan genome, and calculate pan/core genome using bioinformatic tools,
• identify toxins/virulence genes/antibiotics in bacterial genomes using bioinformatics tools.

Reading curriculum, lectures, computer exercises, student presentations and a written assignment.