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The course is a two week (10 days) programme of in-person instruction combining theoretical back with practical instruction and opporunity for hands-on practice of the skills presented.
<style> td, th, table { border: 1px solid black; } td, th {padding-left: 10px; padding-right: 10px; } th { font-weight: bold } .break { background: lightblue; } .weekheader { background: green; color: white } </style>| Week 1 | |||||
| Day 1 (Mon) | Day 2 (Tue) | Day 3 (Wed) | Day 4 (Thu) | Day 5 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Mpox Introduction | Working with example in Epi2Me with Mpox sample | Introduction to Unix/Linux Scripting | Shell programming | Shell programming using fastqc files |
| 11h00 | Tea Break | ||||
| 11h30 | Epi2Me desktop | Working on Epi2Me Mpox results | Working with Consensus Data | Shell programming, Scritpting, Variables cont... | Shell programming using fastqc files cont... |
| 13h00 | Lunch Break | ||||
| 14h00 | Installation and set-up: Epi2Me desktop cont... | Working on Epi2Me Mpox results cont ... | Working with the sandbox Working examples |
Shell scripts | Nextflow |
| Week 2 | |||||
| Day 6 (Mon) | Day 7 (Tue) | Day 8 (Wed) | Day 9 (Thu) | Day 10 (Fri) | |
|---|---|---|---|---|---|
| 09h00 | Phylogenetic trees | fastq data in Epi2Me | Group work on project | Group work on project | Presentations of projects |
| 11h00 | Tea Break | ||||
| 11h30 | Phylogenetic trees session 2 Phylogenetic trees session 3 |
Epi2Me and Genbank database introduction | Group work on project | Group work on project | Presentations of projects |
| 13h00 | Lunch Break | ||||
| 14h00 |
Phylogenetic trees session 4 Phylogenetic trees session 5 |
Phylogenetic figtree visualization tools session 1 Phylogenetic figtree visualization options Session 2 |
Group work on project | Group work on project | Presentations of projects |
This course is being organised by the Africa CDC (the Africa Centres for Disease Control and Prevention), together with the NGS Academy based at CBIO (the Computational Biology Department at the University of Cape Town).