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

12 - 17 November 2017Ho Chi Minh City, Vietnam
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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
  • Programme

    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
  • Instructors / Speakers

    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.

  • How to Apply

    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 / Bursaries

    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.