Practical Course: Bioinformatics Applications in Genome Research

392181 Schulz Block 14.03.2022-25.03.2022 - 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, 14.3. Shell Tizian: Introduction to Python Eric
Tue, 15.3. Assembly Fabian: Genome Assembly, de Brujin Graphs, Tizian: Crash Course Snakemake Pia
Wed, 16.3. Finishing Fabian: BWA Jamie
Thu, 17.3. Genome rearrangements Pia: Rearrangement Distances Fabian
Fri, 18.3. Gene Prediction Eric: Gene Prediction (Software: Glimmer, Prodigal) Tim
Mon, 21.3. Hidden Markov Models (HMMs) Tim: HMMs Jamie
Tue, 22.3. Position-Specific Scoring Matrices (PSSMs) Tim: PSSMs Eric
Wed, 23.3. Haplotype Inference Jamie: WhatsHap Jamie
Thu, 24.3. Metagenomics Pia: Metagenomics Eric
Fri, 25.3. Finishing the Circos plot

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