Working with Pathogen Genomes (Montevideo, Uruguay)

30 November - 04 December 2015Montevideo, Uruguay
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This five-day 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 course will be taught by members of the Pathogen and Parasite Genomics teams from the Wellcome Trust Sanger Institute and regional instructors from Latin American institutes, 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 course will be taught in English.

    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, genome assembly, and
    genome annotation. The course also features a module that aims to teach
    the basics of using genome/gene sequences to plot phylogenetic
    relationships between microbes.

    Please note: The workshop is open to applicants from institutes in Latin America and the Caribbean. Attendance is free of charge for non-commercial applicants and bursaries are available for travel and accommodation expenses

  • 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 course will be taught by members of the Pathogen
    and Parasite Genomics
    teams from the Wellcome Trust Sanger Institute
    and regional instructors from Latin American institutes

  • How to Apply

    Prerequisites
    Applicants should have a molecular biology background. This is a regional
    workshop open to applicants engaged in relevant research in Latin
    American and Caribbean institutes. 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.

    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
    Closed

  • Bursaries

    Bursaries
    Overseas courses are free to attend for non-commercial
    applicants. 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.