A practical introduction to long-read metagenomics data science in the context of the GHPP SGS project 2023.
- 2023-09-25 - Monday: Welcome, Introduction to metagenomics, Linux re-cap
- 2023-09-26 - Tuesday: Nanopore sequencing, data formats, QC, mapping
- 2023-09-27 - Wednesday: Metagenomic read classification
- 2023-09-28 - Thursday: Metagenome assembly, binning, qc, and annotation
- 2023-09-29 - Friday: Final day, Miscellaneous
- Martin Hoelzer (RKI MF1), Hugues Richard (RKI MF1), and Andele Conradie (RKI ZIG)
All events are held at NU, room N04.03.028
| Time | Welcome, Introduction to metagenomics, Linux re-cap |
|---|---|
| 10:00-11:00 | Talk: Long-read Metagenomics (by Josh Quick) |
| 11:00-11:15 | General information |
| 11:15-12:30 | Linux re-cap |
| 12:30-13:30 | Lunch break |
| 13:30-14:00 | Talk: RKI Genome Competence Center (MF1) |
| 14:00-14:30 | Continue Linux re-cap |
| 14:30-15:30 | Hands-on & demo |
| 15:30-16:30 | Wrap-up & self study |
| Time | Nanopore |
|---|---|
| 09:00-10:00 | Debriefing previous day and RKI MF1 intro |
| 10:00-11:00 | Nanopore intro |
| 11:00-11:30 | Nanopore basecalling & data formats |
| 11:30-12:00 | Nanopore QC |
| 12:00-13:00 | Lunch break |
| 14:00-14:30 | Coffee break |
| 14:30-16:00 | Hands-on & demo (metagenomics) |
| 16:00-16:15 | Wrap-up & questions |
| Bonus talks | Metagenomic example projects |
| Time | Metagenomic read classification |
|---|---|
| 09:00-09:30 | Debriefing previous day |
| 09:30-11:00 | Long-read mapping & Hands-on & demo, Part I Mapping |
| 11:00-12:00 | Metagenomic read classification |
| 12:00-13:00 | Lunch break |
| 13:00-14:30 | Hands-on & demo, Part II Classification |
| 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 |
| 10:00-12:00 | Continue Hands-on & demo, Part II Classification |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Metagenome-assembled genomes (MAGs) |
| 14:00-14:30 | Coffee break |
| 14:30-16:00 | Hands-on & demo |
| 16:00-16:15 | Wrap-up & questions |
| Bonus | Detour: 16S Metagenomics introduction and example pipeline |
| Time | The Rest & Open Questions & Work on own data |
|---|---|
| 09:00-10:00 | Debriefing previous day |
| 10:00-12:00 | Work on own data |
| 12:00-13:00 | Lunch break |
| 13:00-14:00 | Continue work on own data |
| 14:00-14:30 | Wrap-up & questions |
| Bonus I | Miscellaneous (bacteria) |
| Bonus II | Hands-on & demo |
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
- Hugues Richard, RKI MF1, metagenomics
- 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
- A. Murat Eren for awesome metagenomics slides and introductions