Genomics is rapidly transforming biomedical research, health, and innovation globally. In Africa, growing investment in infrastructure, data, and networks has created momentum to harness genomics to address local and global health challenges, biodiversity, and development. However, achieving this potential requires coordinated efforts to build research capacity, ensure equitable data generation and access, and strengthen African leadership across the genomics ecosystem.

This inaugural short course is a flagship collaboration between the African Society of Human Genetics (AfSHG), the University of Cape Town (UCT), faculty members from African universities, Wellcome Connecting Science, The Jackson Laboratory, John Hopkins University and a growing network of regional and global partners committed to advancing genomics in Africa. Designed to reflect the continent’s pivotal role in the history and future of genomics, this intensive 10-day residential course brings together early and mid-career researchers from across Africa to build interdisciplinary knowledge, strengthen practical skills, and develop leadership capacity to advance genomics research. Participants will critically explore foundational and emerging topics in genomics, engage in hands-on analysis using accessible tools and datasets, and examine case studies rooted in African-led initiatives. The course will also highlight ethical research practices, with a focus on local and global contexts and how research can be applied equitably.

Through practical sessions, expert-led seminars, peer exchange, and project-based learning, the course will also provide a platform to strengthen networks, nurture innovation, and support participants to become catalysts for sustainable capacity development in their home institutions and countries.

This course is aimed at researchers and clinical professionals based in Africa who are actively engaged in genomics, bioinformatics, or closely related fields. It is particularly suited for early to mid-career scientists, including advanced PhD students, postdoctoral researchers, and healthcare professionals (e.g. clinicians, genetic counsellors, lab scientists) contributing to genomics research or its application in healthcare. Ideal candidates will have some hands-on experience in generating or analysing genomic data, and a demonstrated commitment to strengthening research and training capacity within their institutions or regions.

By the end of the course, participants will be able to:

• Critically evaluate foundational concepts in genomics and bioinformatics in-relation to African research priorities.
• Apply advanced practical skills to generate, analyse, and interpret genomic data using accessible tools and workflows.
• Assess and integrate ethical, equitable, and context-specific considerations into genomics research.
• Analyse the potential and limitations of genomics technologies to advance health and scientific discovery.
• Demonstrate leadership, collaboration, and professional reflective practice to support African genomics capacity.

• Ambroise Wonkam, Johns Hopkins University, USA
• Vicky Nembaware: University of Cape Town, South Africa
• Alice Matimba: Wellcome Connecting Science, UK
• Michelle Bishop: Wellcome Connecting Science, UK
• Rolanda Julius: University of Cape Town, South Africa
• Isabela Malta: Wellcome Connecting Science, UK
• Chandré Oosterwyk-Liu: University of Cape Town, South Africa
• Scarlett Storr: Wellcome Connecting Science, UK
• Kita Magangana: University of Cape Town, South Africa

Visit African Genomics Short Course course page at Wellcome Connecting Science.

The design of the AGSC GitHub organization page was inspired by the Wellcome Connecting Science (WCS) GitHub course page. The main difference between the two designs is that the WCS runs different courses in different iterations each year while the AGSC is a single course run each year. The main design change is therefore the file structure.

In the AGSC, each course directory represents an iteration of the course indicated by the year it was run in. This also means the organization landing page doubles as the main landing page for all the iterations that summarizes the course objectives and activities as oppsed to the WCS which hosts a separate landing page for each course summarizing the course objectives and activities.

In AGSC, the course landing page is simple: it lists the modules, course run information, instructors, and support staff.

A key similarity between the AGSC and WCSC is the Template_Course_Repo repository which contains the template file structure from which each iteration repository can be easily created.

Each course iteration is named AGSC_year (e.g. AGSC_2025).

Below is the file structure for each iteration directory.

.
├── data
│   └── README.md
├── module_1
│   ├── figures
│   │   └── agsc.png
│   └── README.md
...
├── module_7
│   ├── figures
│   │   └── agsc.png
│   └── README.md
├── README.md
└── seminar_slides
    └── README.md

Each course (iteration) directory contains a README.md file that represents the landing page, a data folder, module folders, and a seminar_slides folder. Each folder contains a README.md file describing important information about the content of the folder. Each module folder contains a figures folder for any related visuals.

data:

It contains all relevant data needed to run that iteration. That is all datasets essential for practical exercises and any supplementary data. The data README.md file has guide on preparing content for the data directory and best practices.

module_{1..7}:

Contain the module presentations, manuals, figures, and any supplementary resources, including scripts, ipython notebooks, etc.

Below are best practices for naming module materials:

• File names should be descriptive
• Use lowercase throughout
• Seperate words with underscores
• Include run day and time period: am means morning, pm means afternoon.
• Preferred file formats: PDF and Markdown (therefore convert PowerPoint to PDF to upload to GitHub)
• Examples:
  • foundations_of_genetics_and_genomics_day2_am.pdf
  • sequencing_and_genotyping_workflows_day4_am.md
  • principles_of_evolution_and_popgen_day3_pm.pdf
  • sequence_data_analysis_and_visualization_day5_am.pdf
  • meta-analysis_and_dataset_reuse_day9_pm.md

seminar_slides:

Contains slides from seminars and keynotes for presenters who consent to making their presentations publicly available. It can also contain:

• Supplementary instructional materials (Markdown, PDF)
• Speaker notes (Text files)

Under development