Programme
The course is a two week programme of in-person instruction combining theoretical and practical instruction with an opportunity for hands-on practice of the skills presented.
| Week 1 | |||||
| Day 1 (Mon) | Day 2 (Tue) | Day 3 (Wed) | Day 4 (Thu) | Day 5 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Welcome: What do we hope to achieve? Speed Dating Introductions |
Pathogenwatch wrap-up Talk: Introduction to data visualisation in Microreact |
Applications of Pathogen Genomics Outbreak simulation workshop |
Policy and datasharing Possible Talks (1 or 2 invited speakers) |
Kaptive hands on practical: review and discussion Klebsiella virulence typing part II |
| 11h00 | Tea Break (15 min) | ||||
| 11h15 | Recorded talk: Practical aspects of Pathogen Genomics Pathogenwatch introduction Pathogenwatch practical |
Microreact practical | Outbreak simulation workshop | An introdcution to Klebsiella genomics and strain typing Klebsiella virulence typing part I |
Klebsiella AMR & plasmid typing Kleborate hands on practical |
| 13h00 | Lunch Break | ||||
| 14h00 | Pathogenwatch practical | Microreact Practical & wrap-up Recorded talk: Title TBC (Natacha Couto) |
Outbreak simulation workshop Talk: Genomic surveillance of AMR using amr.watch (Julio Diaz-Caballero) |
Kaptive hands on practical | Kleborate hands on practical |
| 15h15 | Tea Break (15 min) | ||||
| 15h30 - 16:30 | Talk: Genomic surveillance of K. pneumoniae in Europe | Data sharing workflow mapping | Data sharing workflow mapping | Data sharing workflow mapping | Kleborate hands on practical: review & discussion Data sharing workflow mapping |
| Week 2 | |||||
| Day 6 (Mon) | Day 7 (Tue) | Day 8 (Wed) | Day 9 (Thu) | Day 10 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Introduction to CLI: hands-on Theory: File formats, long vs short reads, raw reads QC |
Hands on: variant calling | Cholera case study | Project presentations | |
| 11h00 | Tea Break (15 min) | ||||
| 11h15 | Theory and Hands on; Conda + tool installation | Hands on: phylogenetics | PRACTICAL SESSION: (Trainees to work on projects) | Project presentations | |
| 13h00 | Lunch Break | ||||
| 14h00 | Theory and Hands on QC & alignment | Hands on: phylodynamics | PRACTICAL SESSION: (Trainees to work on projects) | Project presentations | |
| 15h15 | Tea Break (15 min) | ||||
| 15h30 - 16:30 | Theory and Hands on QC & alignment | Hands on: phylodynamics | PRACTICAL SESSION: (Trainees to work on projects) | Project presentations | |
Partners
This course is a joint collaboration between SANBI (the South African National Bioinformatics Institute) at the University of the Western Cape (UWC), Africa CDC (the Africa Centres for Disease Control and Prevention), part of the African Union (AU), African Society for Laboratory Medicine (ASLM), London School of Hygiene and Tropical Medicine (LSHTM) and Big Data Institute at the University of Oxford
