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
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