EACCR2 NID Node Training Course: Genomics
Organisation
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
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
For an introduction to R at the free online site DataCamp click here.
An introduction to R by Emma Rand (at York) is here.
Workshops for Big Data Biology a second year module where we use R are here.
Linux
- A DataCamp free online course in linux is here.
Tutors
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)
Introduction
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.
Workshops
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
Lectures
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)