A practical introduction to ONT, Linux, and bacteria long-read genome reconstruction for NGS Summerschool 2023.
- 2023-08-29 - Tuesday: Welcome, Linux re-cap, QC Nanopore, De novo assembly, mapping
- 2023-08-30 - Wednesday: Final day, Miscellaneous
- Christian Blumenscheit and Martin Hölzer (MF1 Genome Competence Center)
All events are held at Seestraße, house 6 at some room ;)
| Time | Welcome, Linux re-cap, QC Nanopore, De novo assembly, mapping |
|---|---|
| 09:45-10:15 | Welcome & introduction |
| 10:15-11:30 | Linux crash course |
| 11:30-12:00 | Nanopore intro |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Hands on 1: Linux, Mamba, get data, ONT QC |
| 14:00-15:00 | Intro Assembly & Intro Mapping |
| 15:00-16:00 | Hands on 2: de novo Assembly and Mapping |
| Time | Final day & Miscellaneous |
|---|---|
| 09:00-09:30 | Setup & Debriefing Day 1 |
| 09:00-11:30 | Working on own sequencing data |
| 11:30-12:00 | 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