A practical introduction to ONT, Linux, and bacteria long-read genome reconstruction for NGS Summerschool.
- XXXX-XX-XX - Someday: First day: Learn the basic (from raw reads to assembly)
- XXXX-XX-XX - Someday: Final day: Miscellaneous
- ............
All events are held at ..............
| Time | First day: Learn the basic (from raw reads to assembly) |
|---|---|
| 09:00-09:15 | Welcome & introduction |
| 09:15-09:30 | Linux crash course |
| 09:30-10:00 | Hands-on: Setup machines |
| 10:00-10:15 | Coffee break |
| 10:15-11:00 | Hands-on: Data management & ONT QC |
| 11:00-12:00 | Hands-on: Long read assembly |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Hands-on: Polishing with long reads |
| 14:00-14:30 | Bonus: Polishing with short reads |
| 14:30-15:00 | Bonus: Assembly analysis |
| Time | Final day & Miscellaneous |
|---|---|
| 09:00-09:30 | Setup & Debriefing Day 1 |
| 09:00-11:45 | Working on own sequencing data |
| 11:45-12:00 | Wrap up |
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
- 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