A practical introduction to short-read bioinformatics for bacterial genome reconstruction in the context of the Madagascar IGS workshop 2023.
A set of laptops with linux installed will be provided for the lecture. If you want to work with your own laptop, please see the available options below
- 6 October - Friday
- 9 October - Monday
- 10 October - Tuesday
- 11 October - Wednesday
- 12 October - Thursday
- Hugues Richard, Essia Belarbi, Simon Tausch
All events are held at Le Louvre Hotel, Jardin Antaninarenina, 4 Kiana Philibert Tsiranana.
| Time | Linux introduction |
|---|---|
| 14:00-15:30 | Welcome & hands-on with Linux (optional) |
| 15:30-16:00 | Coffee |
| 16:00-17:00 | Hand-on with Linux (follw'd) |
| Time | Linux & NGS |
|---|---|
| 9:00-10:30 | Welcome & introduction |
| 10:30-11:00 | Coffee break |
| 10:30-12:00 | Linux re-cap |
| 12:00-13:00 | Lunch break |
| 13:00-14h30 | Hands-on & Linux exercises |
| 14:30-15:00 | Coffee break |
| 15:00-16:00 | Hands-on (followed) |
| 16:00-16:15 | Wrap-up & questions |
| Time | Manual Raw data QC and analyses |
|---|---|
| 09:00-09:30 | Debriefing Day 1 |
| 09:30-10:00 | Intro NGS technology |
| 10:00-10:45 | Raw data quality control |
| 10:45-11:00 | Coffee break |
| 11:00-12:00 | Hands-on & demo trimming |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Read mapping |
| 14:00-14:30 | Hands-on & demo mapping |
| 14:30-15:00 | Coffee break |
| 15:00-15:45 | Continue practical session |
| 15:45-16:00 | Wrap-up & questions |
| Time | Genome reconstruction and characterization |
|---|---|
| 09:00-10:00 | Debriefing Day 2 |
| 10:00-10:45 | QC and Assembly Lecture |
| 10:45-11:15 | Coffee break |
| 11:15-12:00 | QC and Assembly Hands-on |
| 12:00-13:00 | Lunch break |
| 13:00-13:30 | Functional annotation Lecture |
| 13:30-14:00 | Coffee break |
| 14:00-15:45 | Functional annotation Hands-on |
| 15:45-16:00 | Wrap-up & questions |
| Time | Phylogenetic analyses of isolate sequencing data |
|---|---|
| 09:00-10:00 | Debriefing Day 3 |
| 10:00-11:00 | Phylogenetic analyses Lecture |
| 11:00-12:00 | Phylogenetic analyses Hands-on & demo |
| 12:00-13:00 | Lunch break |
| 13:00-15:00 | Wrap up & questions, Thank you and Goodbye! |
| 15:00-15:15 | Coffee |
- Please fill in the poll for building the follow project here
You can either install a linux distribution as a dual boot or just install windows on linux (WSL). This will allow you to run a linux system within your windows environnment and it is recommended. You can check the installation instructions here (page en français ici )
You will then need to install the required environnments in mamba/conda. The list of environments used for this tutorial is available on this page
This course material is partly based on the following resources and on contributions from great people:
- Carlus Deneke, Federal Institute for Risk Assessment, Germany
- Martin Hölzer, RKI, Germany
- Workshop course template from the MF1 unit at RKI
- Workshop structure inspired by https://github.com/cinemaparis/2023