A practical introduction to long-read bioinformatics for bacterial genome reconstruction in the context of the Kenya MISSIoN project.
- Martin Hölzer, Matt Huska
All events are held at Nordufer, room N01.O2.018
| Time | Linux & Nanopores |
|---|---|
| 10:00-10:30 | Welcome & introduction |
| 10:30-11:00 | Linux re-cap |
| 11:00-12:00 | Nanopore introduction I (intro) |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Nanopore introduction II (file formats & QC) |
| 14:00-14:30 | Coffee break |
| 14:30-16:00 | Hands-on & demo |
| 16:00-16:15 | Wrap-up & questions |
| Time | Genome Reconstruction I |
|---|---|
| 09:00-10:00 | Debriefing Day 1 |
| 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 |
| Time | Genome Reconstruction II & Variant calling |
|---|---|
| 09:00-10:00 | Debriefing Day 2 |
| 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 |
| Time | The Rest & Open Questions |
|---|---|
| 09:00-10:00 | Debriefing Day 3 |
| 10:00-11:00 | Miscellaneous |
| 11:00-12:00 | Hands-on & demo |
| 12:00-12:30 | Wrap-up & questions |
This course material is partly based on the following resources and on contributions from great people:
- Sebastian "Raverjay" Krautwurst, FSU Jena, some Linux and ONT content
- Workshop structure inspired by https://github.com/cinemaparis/2023
- Some ONT intro slides from Josh Quick, original
- Nanopore long-read bioinformatics tutorial from timkahlke