Working with Pathogen Genomes (Cape Town, South Africa)

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

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.

Prerequisites
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
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 contact
us.

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.

Deadlines
Deadline for Applications: Closed

Cost
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.

Bursaries
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.