Practical Course: Bioinformatics Applications in Genome Research

392181 Schulz Block 08.03.2021-19.03.2021 - 9:30-17:30 Uhr via Zoom ekvv


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.

  • Requires participation in the lecture “Algorithms in Genome Research” or similar.
  • Beside regular and active participation in the course, each student gives a short (15min) presentation and presents their results to the other participants.


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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