Course overview/description: The African Bioinformatics Institute will be hosting a Summer School from 08 - 19 June 2026 at the African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE-Uganda), in partnership with the Uganda Virus Research Institute (UVRI), and the MRC/UVRI & LSHTM Uganda Research Unit. The aim is to provide comprehensive training on bioinformatics computational resources, and domain-specific tools and workflows to improve participants' proficiency in executing, interpreting, and communicating analyses for major bioinformatics studies, with a special focus on genomics.

Keywords: Bioinformatics, Genomics, Sequence Data Analysis

Skill level of training: Intermediate

Language: English

Credential awarded: Workshop certificate

Type of training: face-to-face/ in-person training

Venue of workshop: The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE-Uganda).

Dates for the workshop: 8-19 June 2026

Workshop organisers: Shaun Aron, Melek Chaouch, Verena Ras, Jorge da Rocha, David Twesigomwe, Ian Wasukira, Damien Tully, Grace Kebirungi, Sumir Panji, and Nicola Mulder.

Host application link: https://redcap.h3abionet.org/redcap/surveys/?s=3PMCAPYHH9J3LFTY (applications are now closed)

Host applications open: 06 October 2025

Host applications close: 26 October 2025

Successful/unsuccessful hosts informed: 28 February 2026

Participant application link: https://redcap.h3abionet.org/redcap/surveys/?s=YHRD3T97YTMJNNAE (applications are now closed)

Participant application opens: 10 March 2026

Participant application closes: 25 March 2026

Participants informed of outcome: 18 April 2026

Workshop Sponsors: ABI, The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE-Uganda), in partnership with the the Uganda Virus Research Institute (UVRI), and the MRC/UVRI & LSHTM Uganda Research Unit.

Intended Audience:

• MSc/PhD researchers and postdocs from a biology background with baseline bioinformatics experience (Linux, R/Python, basic NGS concepts).
• Research staff/analysts from a biological background who have run at least one bioinformatics related analysis and want to scale up
• Experienced wet-lab scientists, public health and industry staff transitioning into data analysis and meet prerequisites.
• Computer scientists providing bioinformatics support to research groups

Prerequisites:

• Linux CLI basics (cd/ls, file paths)
  • Basic filesystem navigation, file creation, copying, access and modification, use of command line text editor
  • self-test https://swcarpentry.github.io/shell-novice/index.html
• Git usage basics -​​ self test https://swcarpentry.github.io/git-novice/
• R fundamentals - self test https://swcarpentry.github.io/r-novice-gapminder/
  • Basic knowledge of syntax, data loading, structures and manipulation
• Computer scientists providing bioinformatics support to research groups

Syllabus and Tools:

Foundational Skills:

• Linux command line and HPC - introductory to intermediate, sed and awk included
• Programming in R / Intro to Biology (parallel streams for biology/computer science)

Specialised Topics:

• NGS – general
• Domain streams (participants choose one)
  • Pathogen genomics (Module 3A)
  • Human genomics (Module 3B)
  • Metagenomics (Module 3C)

Licensing for course materials: TBC

Learning objectives/outcomes: After this workshop participants should be able to:

• Efficiently navigate and use the Linux command line to set up and run analyses on an HPC environment
• Use Linux command line tools and R programming language to manipulate, analyse and visualise large datasets
• Design, understand and analyse genomic data
• Interpret and communicate analysis results

Workshop Programme:

*Subject to change