A practical introduction to genomic surveillance using SARS-CoV-2 as an example and in the context of the FU course "SARS-CoV-2 Bioinformatics & Data Science" 2024.
- 2024-09-23 - Monday: Welcome, Linux re-cap, container, WMS
- 2024-09-24 - Tuesday: SARS-CoV-2 sequencing & genome reconstruction
- 2024-09-25 - Wednesday: SARS-CoV-2 evolution, mutation profiling & phenotypization
- 2024-09-26 - Thursday: SARS-CoV-2 pathogen evolution & genome-based incidence estimation
- 2024-09-27 - Friday: SARS-CoV-2 phylogeny & outbreak investigation
- Max von Kleist (FU, RKI) and Martin Hoelzer (RKI) & many great colleagues
All events are held at FU Arnimallee 6, Room 017
| Time | Welcome, Linux re-cap, container & WMS |
|---|---|
| 10:00-10:30 | Welcome & course intro |
| 10:30-11:00 | RKI Genomic Surveillance and SARS-CoV-2 |
| 11:00-12:00 | Linux re-cap |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Container & WMS |
| 14:00-14:30 | Coffee break |
| 14:30-16:00 | Hands-on & demo |
| 16:00-16:15 | Wrap-up & questions |
| Time | SARS-CoV-2 sequencing & genome reconstruction |
|---|---|
| 10:00-10:15 | Debriefing previous day |
| 10:15-11:00 | Sequencing (SARS-CoV-2) |
| 11:00-12:00 | SARS-CoV-2 genome reconstruction |
| 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 | SARS-CoV-2 evolution, mutation profiling & phenotypization |
|---|---|
| 10:00-10:15 | Debriefing previous day |
| 10:15-11:00 | SARS-CoV-2 genome organisation & evolution |
| 11:00-12:00 | SARS-CoV-2 epistasis and variants |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | SARS-CoV-2 nomenclature |
| 14:00-14:30 | SARS-CoV-2 mutation profiling |
| 14:30-15:00 | Coffee break |
| 15:00-15:45 | Hands-on & demo |
| 15:45-16:00 | Wrap-up & questions |
| Time | SARS-CoV-2 pathogen evolution & incidence estimation |
|---|---|
| 10:00-10:15 | Debriefing previous day |
| 10:15-10:45 | SARS-CoV-2 Variant prioritization via VOCAL |
| 10:45-11:15 | SARS-CoV-2 Evolution on a Dynamic Immune Landscape |
| 11:15-11:45 | Hands-on (SARS-CoV-2 Evolution on a Dynamic Immune Landscape) |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | SARS-CoV-2 pathogen evolution and genome-based incidence estimation |
| 14:00-14:30 | Coffee break |
| 14:30-15:45 | Hands-on & demo |
| 15:45-16:00 | Wrap-up & questions |
| Time | SARS-CoV-2 phylogeny & outbreak investigation |
|---|---|
| 10:00-10:15 | Debriefing previous day |
| 10:15-12:00 | Phylogeny and outbreak investigation |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Outbreak detection & clustering via breakfast |
| 14:00-14:30 | Coffee break |
| 14:30-15:45 | Hands-on & demo |
| 15:45-16:00 | Wrap-up & questions |
| Time | Project presentations |
|---|---|
| 10:00-11:00 | Project I |
| 11:00-12:00 | Project II |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Project III |
| 14:00-15:00 | Project IV |
| 15:00-16:00 | Project V |
| 15:00-15:15 | Wrap-up |
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
- 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
- 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
- We thank the GISAID initiative for providing a framework for sharing SARS-CoV-2 sequence data internationally and all the submitting labs