Working with Pathogen Genomes (Ho Chi Minh City, Vietnam)

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 Asia and Australasia who are actively involved in,
or soon to commence, relevant research/clinical work. Places are limited
and the course will be taught in English.

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 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
• 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 Asia and
Australasia who are actively involved
in, or soon to commence, relevant
research/clinical work. Please
note that the course will be taught
in English.

Cost
Overseas courses are free to attend for non-commercial applicants. Please
contact us for the commercial fee. Limited bursaries are available to
assist with travel and accommodation costs. Please see the
“Cost/Bursaries” tab for more information.

Applications
Applications for this course can be completed online. 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 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
Overseas courses are 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

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

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.