This training course was organised by organised by the East African Consortium for Clinical Research NID node and the leadership at UVRI/EACCR2.

Includes: Asrat Hailu, Maowia Mukhtar, Erick Muok, Emily Nyanzi, Jaffu Chilongola, Julius Lutwama, Bernard Kikaire, Steve Wandiga, Esther Ngadaya, and Pontiano Kaleebu.

Course facilitators: Asrat Hailu, Tsegahun Manyazewal, Fekadu Abebe

Assisted by: Bethelhem Fekadu, Tesfaye Asefa

EACCR2 is part of the European & Developing Countries Clinical Trials Partnership (EDCTP2) programme supported by the European Union under grant agreement RegNet2015-1104-EACCR2.

Date and Location

University of Gondar, Ethiopia. 29 July – 2 August 2019

Course timetable

Download here


Participants for this first EACCR2 genomics training course came from six Est African countries (Ethiopia, Kenya, Tazania, Sudan, Rwanda and Uganda).

Full list of student institutions Addis Ababa University, Ethiopia Arba Minch University, Ethiopia Bahir Dar University, Ethiopia CDT-Africa, Addis Ababa University Jimma University, Ethiopia Kilimanjaro Christian Medical Centre, Tanzania Kilimanjaro Clinical Research Institute, Tanzania Kenya Medical Research Institute (KEMRI), Kenya Kemri-Wellcome Trust, Kenya Uganda Virus Research Institute University of Gondar, Ethiopia University of Khartoum, Sudan

Other resources for learning

Learning R



All tutors are from The Department of Biology, University of York.

Pete Ashton is the Head of The Genomics & Bioinformatics Laboratory in the Bioscience Technology Facility.

Daniel Jeffares is a lecturer in microbial population genomics.

Sarah Forrester is a postoctoral researcher.

Daniel Jeffares (DJ)

Sarah Forrester (SF)

Pete Ashton (PA)


Welcome to the course. In this course, we will teach some principles and methods of population genomics.

This website contains links to all the course material. We will keep this site available after the course, so you can continue to use it afterwards.


Workshop 1. Analysis of low throughput sequence data and phylogeny creation

Workshop 2. Introduction to linux and servers

Workshop 3. Short read data analysis: quality control, sequence trimming, read alignment and samtools

Workshop 4. Calling and filtering SNPs and indels

Workshop 5. Describing genomic diversity using summary statistics

Workshop 6. Analysis of population structure


Lecture 1. Introduction to genomics (DJ)

Lecture 2. Introduction to next generation and third generation sequencing (PA)

Lecture 3. Processing NGS data files and file processing (SF)

Lecture 4. Principles of population genomics (DJ)

Lecture 5. Introduction to using diversity analysis software (SF)