This is the main repository! If you are planning a new workshop, fork this one and adjust everything you need in your forked repository. If you want to add new content or update existing tools/commands, consider to do these changes first into this main repository via a Pull Request and before you start working on your own workshop specifics!
Below, you find all content of this repository. Please also notice the placeholders "<...>" theat you should adjust!
A practical introduction to <...> for <...> in the context of the <...> project.
- YYYY-MM-DD - SOMEDAY: Nanopore sequencing, data formats, and QC
- YYYY-MM-DD - SOMEDAY: De novo assembly and mapping
- YYYY-MM-DD - SOMEDAY: Assembly polishing and variant calling
- YYYY-MM-DD - SOMEDAY: Final day, Miscellaneous bacteria
- YYYY-MM-DD - SOMEDAY: FU course intro & RKI SARS-CoV-2 genomic surveillance intro
- YYYY-MM-DD - SOMEDAY: SARS-CoV-2 sequencing & genome reconstruction
- YYYY-MM-DD - SOMEDAY: SARS-CoV-2 evolution, mutation profiling & phenotypization
- YYYY-MM-DD - SOMEDAY: SARS-CoV-2 pathogen evolution & genome-based incidence estimation
- YYYY-MM-DD - SOMEDAY: SARS-CoV-2 phylogeny & outbreak investigation
- YYYY-MM-DD - SOMEDAY: Metagenomic read classification
- YYYY-MM-DD - SOMEDAY: Metagenome assembly, binning, qc, and annotation
- <...>, <...>, and <...>
All events are held at <...>, room <...>
| Time | Welcome, Linux re-cap, container & WMS |
|---|---|
| 10:00-10:30 | Welcome & introduction |
| 10:30-12:00 | 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 | Nanopore |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-11:00 | Nanopore intro |
| 12:00-13:00 | Lunch break |
| 13:00-13:30 | Nanopore basecalling & data fromats |
| 13:30-14:00 | Nanopore QC |
| 14:00-14:30 | Coffee break |
| 14:30-16:00 | Hands-on & demo (ONT isolate) |
| 14:30-16:00 | Hands-on & demo (metagenomics) |
| 16:00-16:15 | Wrap-up & questions |
| Time | De novo assembly and mapping |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 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 | Assembly polishing and variant calling |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 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 previous day |
| 10:00-11:00 | Miscellaneous (bacteria) |
| 11:00-12:00 | Hands-on & demo |
| 12:00-12:30 | Wrap-up & questions |
| Time | SARS-CoV-2 Introduction |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-11:00 | FU course intro |
| 11:00-12:00 | RKI Genomic Surveillance and SARS-CoV-2 |
| Time | SARS-CoV-2 sequencing & genome reconstruction |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-11:00 | 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 |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-11:00 | SARS-CoV-2 genome organisation & evolution |
| 10:00-11:00 | SARS-CoV-2 epistasis and variants |
| 12:00-13:00 | Lunch break |
| 10:00-11:00 | SARS-CoV-2 nomenclature |
| 11:00-12:00 | SARS-CoV-2 mutation profiling |
| 14:30-15:00 | Coffee break |
| 13:00-14:30 | Hands-on & demo |
| 15:00-15:45 | Continue practical session |
| 15:45-16:00 | Wrap-up & questions |
| Time | SARS-CoV-2 pathogen evolution & incidence estimation |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-12:00 | SARS-CoV-2 pathogen evolution and genome-based incidence estimation |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | SARS-CoV-2 risk score via VOCAL |
| 14:30-15:00 | Coffee break |
| 13:00-14:30 | Hands-on & demo |
| 15:00-15:45 | Continue practical session |
| 15:45-16:00 | Wrap-up & questions |
| Time | SARS-CoV-2 phylogeny & outbreak investigation |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-12:00 | Phylogeny and outbreak investigation |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Outbreak detection & clustering via breakfast |
| 14:30-15:00 | Coffee break |
| 13:00-14:30 | Hands-on & demo |
| 15:00-15:45 | Continue practical session |
| 15:45-16:00 | Wrap-up & questions |
| Time | Metagenomic read classification |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-12:00 | Metagenomic read classification |
| 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 | Metagenome assembly, binning, and annotation |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-11:00 | Metagenome-assembled genomes (MAGs) |
| 11:00-12:00 | MAG quality and gene annotation |
| 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 |
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, Slides on SARS-CoV-2 nomenclature & phylogeny
- 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
- 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