Disclaimer (delete this in your fork)
This is the main repository! If you are planning a new workshop, fork this one and adjust everything you need in your forked repository. If you want to add new content or update existing tools/commands, consider to do these changes first into this main repository via a Pull Request and before you start working on your own workshop specifics!
Below, you find all content of this repository. Please also notice the placeholders "<...>" theat you should adjust!
Workshop Nanopore Bioinformatics
A practical introduction to <...> for <...> in the context of the <...> project.
Schedule links for the workshop
General
Long-read bacteria genome reconstruction
SARS-CoV-2 data science
Long-read metagenomics
Instructors
Schedule
All events are held at <...>, room <...>
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
| Time |
De novo assembly and mapping |
| 09:00-10:00 |
Debriefing previous day |
| 10:00-10:45 |
De novo Assembly |
| 10:45-11:00 |
Coffee break |
| 11:00-12:00 |
Mapping & Visualization |
| 12:00-13:00 |
Lunch break |
| 13:00-14:30 |
Hands-on & demo |
| 14:30-15:00 |
Coffee break |
| 15:00-15:45 |
Continue practical session |
| 15:45-16:00 |
Wrap-up & questions |
SOMEDAY, DATE
| Time |
Assembly polishing and variant calling |
| 09:00-10:00 |
Debriefing previous day |
| 10:00-10:45 |
Assembly polishing |
| 10:45-11:15 |
Coffee break |
| 11:15-12:00 |
Variant calling |
| 12:00-13:00 |
Lunch break |
| 13:00-14:30 |
Hands-on & demo |
| 14:30-15:00 |
Coffee break |
| 15:00-15:45 |
Continue practical session |
| 15:45-16:00 |
Wrap-up & questions |
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
SOMEDAY, DATE
| Time |
Metagenomic read classification |
| 09:00-10:00 |
Debriefing previous day |
| 10:00-12:00 |
Metagenomic read classification |
| 12:00-13:00 |
Lunch break |
| 13:00-14:30 |
Hands-on & demo |
| 14:30-15:00 |
Coffee break |
| 15:00-15:45 |
Continue practical session |
| 15:45-16:00 |
Wrap-up & questions |
SOMEDAY, DATE
Acknowledgement
This course material is partly based on the following resources and on 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, Slides on SARS-CoV-2 nomenclature & phylogeny
- 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
- Max von Kleist, RKI P5 and FU Berlin, basically most content about sequencing and SC2 data science (evolution, epistasis, incidence esitmation, ...)
- Maureen Smith, Maria Trofimova, RKI P5 and FU Berlin, content on Incidence estimation
- Hugues Richard, RKI MF1, content about SC2 risk assessment
- Matt Huska & Denis Beslic, RKI MF1, content about SC2 outbreak detection & clustering