In this course, practical applications and issues in concrete problem statements and handling real data sets will be addressed. The following topics are intended: assembly, scaffolding, annotation, gene prediction, comparative analysis, etc.
Theoretical knowledge of the students shall be supplemented by practical aspects such as setting up and running existing tools, implementing small own tools, pre- and postprocessing, and critical interpretation of results. A continuously enriched visualization of the data and the obtained results will also guide through the course.
| Date | Topic | Presentation | Solution (for next day) |
| Mon, 8.3. | Shell | Tizian: Introduction to Python | Lisa |
| Tue, 9.3. | Assembly | Nick: Genome Assembly, de Brujin Graphs, Tizian: Crash Course Snakemake | Nick |
| Wed, 10.3. | Finishing | Nele: BWA | Jannis |
| Thu, 11.3. | Genome rearrangements | Lisa: Rearrangement Distances | Nele |
| Fri, 12.3. | Gene Prediction | Nick: Gene Prediction (Software: Glimmer, Prodigal) | Jannis |
| Mon, 15.3. | Hidden Markov Models (HMMs) | Nele: HMMs | Larissa |
| Tue, 16.3. | Position-Specific Scoring Matrices (PSSMs) | Jannis: PSSMs | Jannis |
| Wed, 17.3. | Haplotype Inference | Larissa: WhatsHap | Larissa |
| Thu, 18.3. | Metagenomics | Lisa: Metagenomics | Larissa |
| Fri, 19.3. | Finishing the Circos plot | – | – |
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