A practical introduction to
- Linux for bioinformatics (w/ a focus on
conda/mamba, containers, and workflow management systems) - Nanopore sequencing, bioinformatics, and (long-read) metagenomics
in context of the the third edition of the Eastern European Bioinformatics and Computational Genomics School (EEBG 2024), Suceava, Romania.
- Martin Hölzer, Genome Competence Center, Robert Koch Institute, Germany
All events are held at Universitatea „Ștefan cel Mare” din Suceava
| Time | Welcome, Linux re-cap, container & WMS |
|---|---|
| 11:00-11:15 | Welcome, introduction |
| 11:15-12:00 | Linux re-cap |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Another lecture (Tatiana Tatarinova, University of la Verne, USA) |
| 14:00-15:00 | Container & WMS |
| 15:00-15:45 | Hands-on & demo |
| 15:45-16:00 | Wrap-up & questions |
| Time | Nanopore & metagenomics read classification |
|---|---|
| 09:00-09:30 | Nanopore intro |
| 09:30-09:45 | Nanopore basecalling & data formats |
| 09:45-10:00 | Nanopore QC |
| 10:00-11:00 | Hands-on & demo (nanopore) |
| 11:00-12:00 | Metagenomic read classification |
| 12:00-13:00 | Lunch break |
| 13:00-13:45 | Hands-on & demo (metagenomics) |
| 13:45-14:00 | Wrap-up & questions |
Because we only had limited time, you can find additional material and hands-on examples from previous workshops here:
- A practical introduction to long-read bioinformatics on the flu virus, Namibia, 2024
- A practical introduction to short-read bioinformatics for bacterial genome reconstruction, Madagascar IGS workshop, 2023
- A practical introduction to long-read metagenomics, GHPP "Strengthening Genomic Surveillance" workshop at RKI, 2023
This course material is partly based on the following resources & contributions from great people (no specific order):
- Martin Hoelzer, RKI MF1, content about Linux, container, Nextflow, sequencing, genomic surveillance & glueing everything together
- Sebastian "Raverjay" Krautwurst, FSU Jena, some Linux and ONT content
- Stephan Fuchs, RKI MF1, some Linux and Assembly content
- Matt Huska, RKI MF1, automatic test script for all md code blocks using codedown and general help
- Workshop structure inspired by https://github.com/cinemaparis/2023
- Some ONT intro slides from Josh Quick, original
- Nanopore long-read bioinformatics tutorial from timkahlke
- Hugues Richard, RKI MF1, content about metagenomics
- ... and for sure many other great scientists I forgot to mention (please send a PR!)