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title: "EACCR2 NID Node Training Course: Genomics"
author: ""
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***
<center>
![](pics/EDCTP.png) ![](pics/cdt-africa.png)  

#[![EACCR2.png](pics/EACCR2.png)](http://eaccr.org/) [![](pics/york2.png)](http://www.york.ac.uk)

</center>



***



##Organisation

This training course was organised by organised by the [East African Consortium for Clinical Research](http://eaccr.org/) 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)](http://www.edctp.org/) 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](http://www-users.york.ac.uk/~dj757/popgenomics/pics/popgenomics2019-Ethiopia.pdf)

##Participants

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

<iframe src="https://www.google.com/maps/d/u/0/embed?mid=1qx3GSTpF1c18ncCJsHKs5u6my6hJRpSh" width="640" height="480"></iframe>


**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](https://www.datacamp.com/courses/free-introduction-to-r).

* An **introduction to R** by Emma Rand (at York) is [here](http://www-users.york.ac.uk/~er13/17C%20-%202018/pracs/00Independent_study.html).

* Workshops for **Big Data Biology** a second year module where we use R are [here](http://www-users.york.ac.uk/~dj757/BIO00047I/BIO00047I_index.html).


**Linux**

* A **DataCamp** free online course in linux is [here](https://www.datacamp.com/courses/introduction-to-shell-for-data-science).

***

##Tutors

All tutors are from [The Department of Biology, University of York.](https://www.york.ac.uk/biology/)

**Pete Ashton** is the Head of [The Genomics & Bioinformatics Laboratory](https://www.york.ac.uk/biology/technology-facility/genomics/) in the [Bioscience Technology Facility](https://www.york.ac.uk/biology/technology-facility/).

**Daniel Jeffares** is a lecturer in [microbial population genomics](http://www.jeffareslab.org).

**Sarah Forrester** is a [postoctoral researcher](https://orcid.org/0000-0001-8332-7196). 

<br/> 
![](pics/daniel-jeffares.jpg)
<br/>
**Daniel Jeffares (DJ)**
<br/> 



<br/> 
![](pics/sarah-forrester.jpg)
<br/>
**Sarah Forrester (SF)**
<br/>


<br/> 
![](pics/peter-ashton.jpg)
<br/>
**Pete Ashton (PA)**
<br/>


***

## 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](http://www-users.york.ac.uk/~dj757/popgenomics/workshop1.html)

**Workshop 2.** [Introduction to linux and servers](http://www-users.york.ac.uk/~dj757/popgenomics/workshop2.html)

**Workshop 3.** [Short read data analysis: quality control, sequence trimming, read alignment and samtools](http://www-users.york.ac.uk/~dj757/popgenomics/workshop3.html)

**Workshop 4.** [Calling and filtering SNPs and indels](http://www-users.york.ac.uk/~dj757/popgenomics/workshop4.html)

**Workshop 5.** [Describing genomic diversity using summary statistics](http://www-users.york.ac.uk/~dj757/popgenomics/workshop5.html)

**Workshop 6.** [Analysis of population structure](http://www-users.york.ac.uk/~dj757/popgenomics/workshop6.html)


***


## Lectures

**Lecture 1.** [Introduction to genomics](http://www-users.york.ac.uk/~dj757/popgenomics/lectures/lecture1.pdf) (DJ)

**Lecture 2.** [Introduction to next generation and third generation sequencing](http://www-users.york.ac.uk/~dj757/popgenomics/lectures/lecture2.pdf) (PA)

**Lecture 3.** [Processing NGS data files and file processing ](http://www-users.york.ac.uk/~dj757/popgenomics/lectures/lecture3.pdf) (SF)

**Lecture 4.** [Principles of population genomics](http://www-users.york.ac.uk/~dj757/popgenomics/lectures/lecture4.pdf) (DJ)

**Lecture 5.** [Introduction to using diversity analysis software ](http://www-users.york.ac.uk/~dj757/popgenomics/lectures/lecture5.pdf) (SF)


***




