- Location: [Location]
- Information:
- Primal Scheme website: https://labs.primalscheme.com/
- Rerun your samples with new inputs. Use ‘fetch’ method in galaxy upload:
https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_v430.tar.gz https://raw.githubusercontent.com/quick-lab/primerschemes/refs/heads/main/primerschemes/artic-inrb-mpox/2500/v1.0.0-cladeiib/reference.fasta https://raw.githubusercontent.com/quick-lab/primerschemes/refs/heads/main/primerschemes/artic-inrb-mpox/2500/v1.0.0-cladeiib/primer.bed
| Time | Activity | Presenter | |
|---|---|---|---|
| 9:00 – 9:10 | Recap and the day’s activities | Ammar | |
| 9:10 – 9:30 | 5 - Lecture - QC of consensus sequences | Kristy/Ammar | |
| 9:30 – 10:00 | 5 - Hands on - QC on consensus sequences | Kristy/Ammar | |
| 10:00 – 10:30 | Morning tea | ||
| 10:30 – 11:00 | 6 - Lecture - Introduction to Nextclade | Kristy/Ammar | |
| 11:00 – 11:30 | 6 - Hands on - Nextclade for Lineages and QC | Kristy/Ammar | |
| 11:00 – 12:00 | Hands-on: Using public genomic databases | Ammar | |
| 12:00 – 13:00 | Lunch | ||
| 13:00 – 13:30 | Lecture: Introduction to phylogenetics | Wytamma | |
| 13:00 – 13:30 | Lecture: Introduction to phylogenetics EXTRA | Wytamma | |
| 13:30 – 14:00 | Demo: Constructing a Phylogenetic Tree | Wytamma | |
| 14:00 – 14:30 | Introduction to Nextstrain | Wytamma | |
| 14:30 – 15:00 | Afternoon tea | ||
| 15:00 – 17:00 | Hands-on: MPXV Phylogenetics | Wytamma | |
| 17:00 – 17:10 | Wrap up | MC |
Nextclade work around: https://colab.research.google.com/drive/1upJsh0_V4oKHPB7v825BUg2HYf9OvbUh?usp=sharing