Workshop structure
Modules
The workshop is formulated to be a 5-day hands-on training, covering both wet-lab and bioinformatics methods for viral genome sequencing and analysis. It will combine lab-based, and interactive classroom-based sessions on data analysis and interpretation. Participants will use a simulated outbreak scenario to mimic real-world observations.
The following modules will be covered:
- Introduction to genomic epidemiology
- Introduction to nanopore sequencing and ARTIC protocols
- Simulated outbreak scenario
- Consensus building and quality controls
- Introduction to phylogenetic analysis
- Showcase of ONT MinION flow cells and software (MinKNOW, EPI2ME)
- Hands-on lab sessions covering ONT library methodology, including multiplex PCR, SPRI cleanups, end-preparation, barcode ligation, adapter ligation, final library preparation, flow cell priming, and sequencing
- Sequencing monitoring and diagnosing problems
- Hands-on bioinformatics sessions running ARTIC amplicon-nf and raccoon-nf
- Phylogenetic tree interpretation
- WACCBIP journal club
- Real world implementation of the workflow (title TBC)
- Participants’ presentations
Schedule (subject to change)
| Time | 2026-03-26 - Thursday | 2026-03-27- Friday | 2026-03-28 - Saturday | 2026-03-29 - Sunday | 2026-03-30 - Monday | 2026-03-31 - Tuesday |
|---|---|---|---|---|---|---|
| 08:30 - 09:00 | Arrival | Arrival | Arrival | Free day | Arrival | Arrival |
| 09:00 - 09:30 | Introductions - WACCBIP, ARTIC, Instructors & participants | Recap of day 1 & Overview of next steps in lab protocol | Recap of day 2 & Overview of next steps | – | Recap of day 3, sequencing output | Recap of the week |
| 09:30 - 10:00 | WACCBIP introductions / health & safety | Theory of SPRI, EP, barcoding | Demo/showcase of ONT flow cells, MinION, MinKNOW, EPI2ME | – | Overview of Consensus building and QC | Troubleshooting (wet-lab, ampicon-nf, tree) |
| 10:00 - 10:30 | [continued] | [continued] | Laptop clinic | – | Computational session 1: amplicon-nf | [continued] |
| 10:30 - 11:00 | Coffee break | Coffee break | Coffee break | – | Coffee break | Coffee break |
| 11:00 - 11:30 | Course overview | Lab session 2: PCR pooling, cleanup, quantification | Lab session 4: adapter ligation, cleanup, library prep, flow cell checks, priming, loading; flow cell loading practice | – | Computational session 1 [continued] | Journal club (WACCBIP) |
| 11:30 - 12:00 | Introduction to genomic epidemiology | [continued] | [continued] | – | [continued] | [continued] |
| 12:00 -12:30 | [continued] | [continued] | [continued] | – | [continued] | Real world applications talk (title TBC) |
| 12:30 - 13:00 | Outbreak scenario overview | [continued] | [continued] | – | [continued] | [continued] |
| 13:00 -13:30 | Lunch break | Lunch break | Coffee break | – | Lunch break | Lunch break |
| 13:30 - 14:00 | Lunch break | Lunch break | Coffee break | – | Lunch break | Lunch break |
| 14:00 - 14:30 | Intro to nanopore sequencing and ARTIC protocol overview | Lab session 3: EP, Barcoding, cleanup | Flow cell loading (demo in lecture theatre) | – | Intro to phylogenetic analysis | Participant presentations |
| 14:30 - 15:00 | [continued] | [continued] | Sequencing monitoring, diagnosing problems | – | Computational session 2: Alignment & Phylogenetics practical using raccoon-nf | [continued] |
| 15:00 - 15:30 | Principles of sample quality and sample preparation | [continued] | [continued] | – | [continued] | [continued] |
| 15:30 - 16:00 | Coffee break | Coffee break | Laptop clinic | – | Coffee break | Coffee break |
| 16:00 - 16:30 | Group allocation | Lab session 3 [continued] | Networking session | – | Tree interpretation | Feedback forms & post-workshop quiz |
| 16:30 - 17:00 | Lab session 1: samples, multiplex PCR | [continued] | [continued] | – | Computational session 2 [continued] | Wrap up and Certificates |
| 17:00 - 17:30 | [continued] | [continued] | [continued] | – | [continued] | [continued] |
| 17:30 - 18:00 | [continued] | [continued] | [continued] | – | [continued] | – |
| 18:00 - 18:30 | [continued] | – | – | – | – | – |
Resources
Scenario materials
Details of the scenario can be found in the factsheet and sitreps, as well as the map of the fictional country Articia that will be provided during/before the workshop.
Slide decks
All slide decks will be made available after the workshop.
Protocols and tutorials
Wet-lab protocol
The wet-lab protocol is based on the ARTIC LoCost protocol. It describes the workflow starting with the multiplex PCR, end preparation and barcode ligation, adapter ligation, and preparing the library for loading on ONT flow cells. Samples processed from different groups are pooled together into a library to maximise efficiency and resources allocation.
The primer scheme used in this protocol can be found in primalscheme labs.
ARTIC Amplicon-nf tutorial
ARTIC Raccoon-nf tutorial
You can access the phylogenetics tutorial that uses raccoon-nf here.
Example outputs
Example output data will also become available after the workshop.