ABI Summer School 2026

Materials for the Summer School 08 - 19 June 2026

About the event:

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.

Course Content:

Week 1:

Linux and High Performance Computing

  1. Introduction to Linux & HPC
  2. Linux Basics Recap
  3. Bash Scripting I & HPC Job Submission
  4. File processing with sed
  5. File processing with awk
  6. Bash Scripting II
  7. Containers
  8. Day One Assignment

R programming

Intro to NGS

Week 2

Human Genomics

  1. [Introduction to Human Genomics: Overview of Data QC and Analysis Workflow]
  2. [Practical: Read alignment using BWA-MEM and QC]
  3. [Principles of Human Variant Calling]
  4. Variant Calling Practical using GATK HaplotypeCaller
  5. [Variant Filtering and Exploration — Single-sample and Multi-sample VCF Files]
  6. [Introduction to Workflow Automation using Nextflow]
  7. [Practical: Human Variant Calling Workflow Automation using Nextflow]
  8. [Principles of Variant Annotation and Variant Effect Prediction]
  9. [Practical: Variant Annotation/Prioritisation]
  10. [Statistical Phasing Concepts and Practical Example using 1000 Genomes Project data]
  11. [Overview of long-read sequencing technologies and data analysis tools]
  12. Practical: Oxford Nanopore read alignment and variant calling
  13. [Introduction to Structural Variation Analysis]
  14. [Practical: Structural variant calling and annotation]
  15. [Course assessment]

Pathogen Genomics

  1. Basics of Bacterial Genomes
  2. Quality Control of Sequencing Data
  3. Assembly Principles: Reference Vs De Novo
  4. Genome Alignment & Variant Calling
  5. Bacterial Genome Annotation
  6. Pan-genome Analysis & Multilocus Sequence Typing
  7. Mechanisms of AMR & Virulence
  8. Horizontal Gene Transfer & Mobile Genetic Elements
  9. Applications of Bacterial Genomics: AMR Surveillance

Metagenomics

  1. Quality Control
  2. Amplicon Data Analysis
  3. Diversity Analysis
  4. Shotgun Metagenomics
  5. Metagenome-Assembled Genomes
  6. Functional Analysis
  7. Visualisation & Mini-Project

Trainer Info

Name Affiliation Role Stream
Gloria Nakabiri African Center of Excellence in Bioinformatics and Data Intensive Sciences Lead trainer Unix
Peter van Heusden South African National Bioinformatics Institute (SANBI) Lead trainer R
Ian Wasukira African Center of Excellence in Bioinformatics and Data-Intensive Sciences Lead Trainer Unix/HPC
Ronald Galiwango African Center of Excellence in Bioinformatics and Data-Intensive Sciences Lead trainer R
Musalula Sinkala University of Cape Town Lead trainer Human Genomics
Dayna Adrienne Croock Stellenbosch University Lead trainer Human Genomics
John Juma International Livestock Research Institute (ILRI) Lead trainer Pathogen Genomics
Damien Tully MRC/UVRI & LSHTM Uganda Research Unit Lead Trainer Pathogen Genomics
Alfred Ssekagiri Uganda Virus Research Institute Lead trainer Metagenomics
Yohannes Gedamu Gebre Bio and Emerging Technology Institute (BETin); former Ethiopia Biotechnology Institute (EBTi) Co-trainer Unix/R/Pathogen Genomics
Keaghan Brown PHA4GE Co-trainer Pathogen Genomics
Amadou Diallo Pioneer Bio-Analytics Co-trainer Metagenomics
Ephifania Geza University of Cape Town Lead trainer Metagenomics
Patricia Nabisubi The African Centre of Excellence in Bioinformatics and Data Intensive Sciences Co-trainer Unix/R/NGS basics
Trushar Shah International Livestock Research Institute (Kenya) Co-trainer Human Genomics/Unix
Daria Sokolova European Bioinformatics Institute (EBI) Core organiser/support
Grace Kebirungi African Center of Excellence in Bioinformatics and Data-Intensive Sciences Core organiser/support
David Twesigomwe MRC/UVRI & LSHTM Uganda Research Unit Core organiser/support
Verena Ras African Bioinformatics Institute / University of Cape Town Core organiser/support
Shaun Aron Sydney Brenner Institute for Molecular Bioscience (SBIMB) / University of Witwatersrand Core organiser/support
Melek Chaouch Institut Pasteur, Tunis Core organiser/support
Jorge da Rocha European Bioinformatics Institute (EBI) Core organiser/support