Bioinformatics analysis of the monkey pox virus

Workshop - Accra, Ghana, July 2026

This repository contains the materials and documentation for the workshop on the bioinformatics of the monkey pox virus

Instructors

• Marie Lataretu
• Torsten Houwaart

Schedule

Day 01 | 2026-07-28 | Tuesday

Linux introduction, terminal basics, navigation, file management, viewing files, editing text.

Time	Activity
09:00 - 12:00	Check-in & Laptop set up
12:00 - 13:00	🍽️ Lunch Break
13:00 - 16:30	Linux CLI

Day 02 | 2026-07-29 | Wednesday

Time	Activity
09:00 - 09:45	Recap
09:45 - 12:00	Trimmomatic (with coffee break in between)
12:00 - 13:00	🍽️ Lunch Break
13:00 - 16:30	BWA mem and Freebayes (with coffee break in between)

Day 03 | 2026-07-30 | Thursday

Time	Activity
09:00 - 09:30	Recap
09:30 - 09:45	Pipelines and workflow manager
09:45 - 10:30	Genome reconstruction with amplicon-nf
10:30 - 10:45	☕ Break
10:45 - 12:00	Downstream analysis I: Nextclade
12:00 - 13:00	🍽️ Lunch Break
13:00 - 14:30	Downstream analysis II: Phylogenetic trees
14:30 - 15:30	Data analysis
15:30 - 16:00	Recap & Closing remarks

Recommended setup

Clone the repository into your home directory:

cd ~
git clone https://github.com/rki-mf1/2026-Workshop-Ghana.git
cd ~/2026-Workshop-Ghana

How to use this repository

• Start at the README.md of the relevant day.
• Follow the exercises in numerical order.
• Use a scratch or practice directory when a lesson asks you to create, move, rename, or delete files.