Pan African Bioinformatics Network for H3Africa

Working with Pathogen Genomes

Venue of workshop: University of Cape Town Health Science Faculty, Cape Town, South Africa

Dates for the workshop: 17th to 22nd June 2018

Understanding pathogen genomes, how they evolve and which genes are essential for their ability to cause disease, is a key part of the battle to reduce the global disease burden.

This five-day computational course aims to give molecular microbiologists working with bacterial and eukaryotic pathogens a working knowledge of genomic analysis. The course will be taught by members of the Infection Genomics teams from the Wellcome Trust Sanger Institute in collaboration with regional instructors and speakers, and will take the form of a series of modules covering the fundamental aspects of DNA sequence analysis and exploitation.

Each module will be introduced with a short talk, followed by hands-on worked examples using data from bacterial and eukaryotic pathogens. A key aspect of this course is the shared interest in pathogens between instructors and participants. This common understanding of the questions and problems presented by our work results in particularly fruitful interactions.

The course begins with training in the use of genome analysis software (Artemis and ACT), developed at the Sanger Institute for genome exploration and comparative genomics. It then goes on to cover the mapping of Illumina sequence data, SNP calling, phylogenetics, genome assembly, genome annotation and RNA-seq.

The course is aimed at scientists or clinicians/healthcare professionals based in institutes in Africa who are actively involved in, or soon to commence, relevant research/clinical work. The course is free to attend and limited bursaries are available to cover travel and accommodation expenses. All modules will be taught in English.

The programme will include lecture and practical computer-based sessions covering the following topics:

  •     Introduction to pathogen genomics
  •     Introduction to Artemis
  •     Using the Linux operating system for bioinformatics
  •     Comparative genomics using the Artemis Comparison Tool (ACT)
  •     Mapping Illumina sequence data against a reference genome
  •     Genome-wide phylogenetic analysis using SNPs
  •     Genome assembly
  •     Genome annotation
  •     Transcriptome analysis using RNA-seq data
  •     Two extended practical sessions applying the above topics

Learning Outcomes
After completing this course, participants should be able to:

  •     Understand the different file formats related to genome sequencing data
  •     Explore genome sequences using Artemis
  •     Map sequencing reads to a reference genome
  •     Identify genomic differences between pathogens
  •     Construct phylogenetic trees to understand the recent evolution of pathogens
  •     Produce new, annotated genome sequences
  •     Identify changes in pathogen gene expression

Applicants should be scientists or clinicians/healthcare professionals based in institutes in Africa who are actively involved in, or soon to commence, relevant research/clinical work. The course will be taught in English.

Applications can be submitted online. Places are limited and will be awarded on merit. If you have any problems with the online application process, please This email address is being protected from spambots. You need JavaScript enabled to view it. .

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager, or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

Deadline for Applications: 2 March 2018

The course is subsidised by the Wellcome Genome Campus Advanced Courses and Scientific Conferences Programme and is free to attend for non-commercial applicants. Please contact us for the commercial fee.

Limited bursaries to cover travel, accommodation and sustenance costs are available and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application

Bursary terms and conditions

Overseas Courses (held outside of the UK)
A limited number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance. The maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.