Course Overview: The workshop involves theoretical lectures and practical sessions on analysis techniques for dealing with Next Generation Sequencing (NGS) data, including an introduction to programming for the study of large data sets of HIV and other genomic data. It will introduce working in Linux and R statistical programming. Various topics on NGS analysis e.g. de novo genome assembly, annotation, SNP calling, HIV-1 drug resistance mutation genotyping, population genetics/phylogenetics etc will be covered. Tools for data visualization and analysis e.g. Galaxy, e-Biokit among others will also be introduced. Usage of open source technologies will be encouraged.

Intended Audience: Designed for Scientists, graduate students, postdoctoral research fellows, and exceptional undergraduates in the region to become familiar with NGS data handling and analysis techniques.

Keywords: Genetics, Genomics, Nucleic acid analysis

Skill level: Beginner

Language: English

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

Venue of workshop: Uganda Virus Research Institute, Entebbe Uganda

Dates for the workshop: 6th to 10th July 2015.

Workshop organisers:  MUIITHRiVEAfrica Centre for Health and Population Studies Wellcome Trust ProgramsH3ABioNet , MRC/UVRI Uganda Research Unit on AIDS, and the Uganda Virus Research Institute

Registration opens:  8th May, 2015

Registration closes: 8th June, 2015

Notification date: 12th June, 2015

Link to application form:

Participation: Application open to in-country H3Africa/H3ABioNet consortium and UVRI-Node research partners with selection, giving priority to those with demonstrated need for this training. A total of 25 participants from all the applications received will be selected.

Workshop SponsorsMUII and THRiVE


Syllabus and Tools: Participants will learn about Linux, R programming, NGS assembly, annotation, and population genetics of genomes using various data visualization and analysis tools.

Trainers and support staff: 
Deo Ssemwanga, (MRC/UVRI, Entebbe, Uganda)
Jonathan Kayondo, (UVRI, Entebbe, Uganda)
Fred Lyagoba, (UVRI, Entebbe, Uganda)
Benard Kulohoma, (ICIPE, Nairobi, Kenya)
Justen Manasa, (WT Africa Centre for Health and Population Studies, South Africa)
Anne Derache, (WT Africa Centre for Health and Population Studies, South Africa) 
Etienne Villiers, (KEMRI/ Wellcome Trust, Kilifi, Kenya)
Miguel Quinones-Mateu,( Case Western Reserve University, Cleveland , USA)
Pontiano Kaleebu, (MRC/UVRI, Entebbe, Uganda)
Tulio de Oliveira (WT Africa Centre for Health and Population Studies, South Africa)

Prerequisites:  Participants will need to work through the following resources to enable them to gain the most from the workshop:

Objectives:  The objective is to introduce bioinformatics analysis techniques for dealing with Next Generation Sequencing (NGS) data. After this workshop participants should be able to:
- Attempt using Linux based platforms for analysis
- Have a good familiarity with R and conducting statistical tests within R
- Assemble and analyze NGS genome data 
- Perform HIV-1 drug resistance mutation genotyping
- Perform various phylogentics analysis for viral transmission, evolution and other studies
- Use the e-Biokit and other resources for bioinformatics analysis

Workshop limitations: This workshop will only provide a foundation for continued learning in NGS bioinformatics and will not make you an expert in bioinformatics or NGS analysis.

Registration: All potential applicants must complete the application form and obtain and attach a motivation letter from their supervisor / Head of Department and submit the application form according to the instructions contained within it. Incomplete applications will NOT be reviewed. The successful applicants for the workshop will be contacted to complete a short biosketch with a recent picture and Participants will also be requested to come to the workshop with a poster describing their research.

Questions: If you may have any further queries, please contact Dr. Jonathan Kayondo

Training Materials Availability:

Training materials for this course are not currently available.