Nanopore Sequencing-based Study of Microorganisms

This is a block (pro)seminar covering topics related to nanopore sequencing-based studies of microorganisms. This emerging sequencing technology holds great promise for the fast and cost-effective analysis of microorganisms. However, several challenges need to be overcome. In this pro/seminar, we will be covering (mostly) the computational side of challenges, including base calling, detection of base-modifications, error-correction, and assembly.

Tutor: Cedric Laczny


Registration from April 19th, 2017 to April 26th, 2017 HERE
Kick-off meeting [optional] 26th June 2017 at 16:00 c.t. in E2.1, room 206
Deadline to register in HISPOS 17th July 2017
De-registration deadline 17th July 2017
Deadline for feedback * [optional] 29th July 2017
Presentations 29th August 2017 at 09:00 c.t. in E2.1, room 206
Summary submission deadline 5th September 2017

* If you would like to get feedback about your slides, e.g. to improve your presentation before the talk, send your slides to the tutor before the feedback deadline. We strongly encourage you to take this opportunity. Before sending in the slides, check out our presentations guidelines (presentation guidelines, presentation guidelines checklist). Please note: The more complete the submitted presentation the more helpful the feedback can be. Please try to avoid submitting half-finished slides.

Hint Your slides will make up a substantial part of the final grade. Reading and paying attention to the provided presentation guidelines (see above) will help you to get an impression of which aspects are relevant for the evaluation. Disregarding many of the points listed in the guidelines may negatively affect your grade.

Place and Time:

  • E2.1, room 206, TBD

Requirements for participation:

  • Proseminar: at least in 3rd semester, Bioinformatics I

Certificate requirements:

  • Successful presentation:
    • Talk: 30 minutes (proseminar); 40 minutes (seminar)
    • Questions from the audience after the presentation
  • Attendance to all presentations
  • Submitting a summary (can have an impact on the final grade):
    • Short description of the presented topic(s)
    • Ca. 2 pages of text, i.e. excluding title (page), references, figures, tables etc.
    • No figures or tables required
    • Main structure: title page, main text, references

Final grade:

  • Based on the given presentation (see “Certificate requirements”)
  • May be influenced by the submitted summary


Nr. Presentation Topic Participant
1 Seminar Rapid resistome mapping using nanopore sequencing Nadja G.
2 Seminar Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology Ilkay U.
3 Seminar Real-time selective sequencing using nanopore technology Elnaz M.
4 Seminar Detecting DNA cytosine methylation using nanopore sequencing Andres S.
5 Proseminar Nanocall: an open source basecaller for Oxford Nanopore sequencing data Mohammed A.
6 Seminar Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome
Sophian G.