Working with Pathogen Genomes

20-24 February 2012

Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok

Now closed for applications. To be kept updated on dates for the 2013 course, please email us.

This five-day workshop aims to give molecular microbiologists a working knowledge of genomic analysis, which will cover the handling and processing of DNA sequence and transcriptomic data produced by ‘second generation’ sequencers. The workshop will be taught by members of the Wellcome Trust Sanger Institute Pathogen Genomics team and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Modules will be introduced with a short talk, followed by 'hands on' worked examples using bacterial and small eukaryotic pathogens.

The workshop begins with training in the use of genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute for genome exploration and comparative genomics. It then goes onto cover the mapping of Illumina sequence data and calling and recording SNPs and other sequence variation data. The course also features a module that aims to teach the basics of using genome/gene sequences to plot phylogenetic relationships between microbes, as well as an introduction to Perl programming for basic processing and mining of data.

Programme

Introduction to genomics and Artemis

Overview of genome sequencing strategies, assemblies and genome analysis
Understanding DNA sequence data formats
Using Artemis as a sequence analysis tool for prokaryote and small eukaryotic genomes

De novo sequence analysis

Transfer of annotation from reference genomes
Gene prediction and the construction of gene models
RNA-Seq data for transcriptomic analysis and confirming gene models
Using public databases to add value to gene prediction
Principles and application of motif and domain searches
Using web based sequence analysis tools

Comparative genomics

Extensive hands on experience of the Artemis genome Comparison Tool (ACT)
Mapping and re-ordering of draft assemblies against a reference
Mapping of Illumina sequence data against a reference
Calling and viewing variation data
Phylogenetic analysis using SNPs

General bioinformatics skills

Introduction to the UNIX operating system
Basic Perl programming for processing genomic data

How to apply

Prerequisites
Applicants should have a molecular biology background and currently be engaged in relevant research.

Cost
The course is subsidised by The Wellcome Trust and there is no course fee for non-commercial applicants. The fee for commercial applicants is £1000.

Bursaries
Bursaries are available for non-commercial applicants to cover travel and accommodation costs.These are subject to a selection process and are awarded on merit. The amount awarded will depend on the number of applicants. Please see our bursaries page for application information and terms and conditions.

Applications
Applicants will be required to complete an application form containing a 300-word outline of the relevance of the course to their research. Please note that documentation supporting their application will be required from the applicant's supervisor/head of department.

To submit an application, please either:

Applications can be accepted by post or email. Sponsors' supporting letters must be returned, signed, by fax or post under separate cover. Please note: Incomplete applications will be rejected.

Applications and letters of support should be sent to:

Wellcome Trust Advanced Courses
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire CB10 1SA
UK
F +44 (0) 1223 495130
E opendoor@hinxton.wellcome.ac.uk

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888