This course type is computational

Working with Pathogen Genomes

17 - 22 January 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This five-day computational workshop aims to give molecular
    microbiologists working with bacteria and eukaryotic pathogens a working
    knowledge of genomic analysis, which will cover the handling and
    processing of DNA sequence data produced by ‘second generation’
    sequencers. The workshop will be taught by members of the Pathogen
    and Parasite Genetics teams
    from the Wellcome Trust Sanger Institute
    and will take the form of a series of modules covering most aspects of
    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.

    The workshop begins with training in the use of genome analysis software
    (Artemis and
    ), 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, genome assembly, and genome annotation. The
    workshop also features a module that aims to teach the basics of using
    genome/gene sequences to plot phylogenetic relationships between

    Feedback from previous workshops
    “This was an incredible course–very well organized and a thorough
    mix of lectures and computer labs. The instructors were amazing and so
    “A really excellent course with superb access to expertise. Can’t fault
    it in any way.”
    “Thank you! This course was invaluable to me. I left feeling re-energized
    and much better informed about tools for genome exploration.”
    “Great course! Probably one of the best courses I’ve attended.”

  • Programme

    The programme will include lecture and practical computer-based sessions
    covering the following topics:

    Introduction to Artemis/ACT
    and comparative genomics

    • Using Artemis as a sequence analysis tool for prokaryote and eukaryotic genomes
    • Extensive hands on experience of the Artemis genome Comparison Tool (ACT)
    • Overview of genome sequencing strategies, assemblies and genome analysis
    • Understanding DNA sequence data formats
    Analysis of genomic sequencing data
    • Mapping Illumina sequence data against a reference genome
    • Genome-wide phylogenetic analysis using SNPs
    • De novo genome assembly from short reads
    • Annotating your genome assembly using ab initio gene finders
  • Instructors / Speakers

    The workshop will be taught by members of the Pathogen and Parasite Genetics teams from the Wellcome Trust Sanger Institute.

  • How to Apply

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

    The workshop is subsidised by the Wellcome Genome Campus
    Advanced Courses and Scientific Conferences Programme. This is a
    residential workshop and there is a fee of £690 towards board and lodging
    for non-commercial applicants. Please contact us for the commercial fee.

    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.


  • Bursaries

    Advanced Courses are subsidised for non-commercial
    applicants from anywhere in the world. Additional, limited bursaries are
    available (up to 50% of the course fee) and are awarded on merit. If you
    would like to apply for a
    bursary, please complete the bursary section
    of the online application

    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,
    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

    Overseas Courses (held outside of the UK)
    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.
    will be notified of a bursary award along with their place on
    course, usually within one month of the application deadline. The
    decision of the selection committee is