Practical Course: Bioinformatics Applications in Genome Research

392181 Schulz Block 06.03.2022-17.03.2022 - 9:30-17:30 Uhr 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, 06.3. Shell Tizian: Introduction to Python and Unix Shell Diego
Tue, 07.3. Assembly Marco: Genome Assembly, de Brujin Graphs, Tizian: Crash Course Snakemake Marco
Wed, 08.3. Finishing Wanja: BWA Wanja
Thu, 9.3. Genome rearrangements Diego: Rearrangement Distances Diego
Fri, 10.3. Gene Prediction Diego: Gene Prediction (Software: Glimmer, Prodigal) Marco
Mon, 13.3. Hidden Markov Models (HMMs) Wanja: HMMs Wanja
Tue, 14.3. Position-Specific Scoring Matrices (PSSMs) Marco: PSSMs Marco
Wed, 15.3. Haplotype Inference Diego: WhatsHap Diego/Wanja
Thu, 16.3. Metagenomics Wanja: Metagenomics Marco
Fri, 17.3. Finishing the Circos plot

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