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Next Generation Sequencing Bioinformatics (Johannesburg, South Africa)

27 January - 01 February 2019University of Witwatersrand, Johannesburg, South Africa
Deadlines (at 23:59 UTC):
  • Application and bursary deadline 11 October 2018
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Hands-on introduction to bioinformatics for next generation sequencing.

  • Summary

    In collaboration with the H3Africa Bioinformatics Network and the University of the Witwatersrand, Johannesburg, South Africa, we are pleased to announce our latest Overseas Course in Next Generation Sequencing Bioinformatics.

    Next generation sequencing has become an essential tool in current genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to assess and analyse the large volumes of sequencing data produced by next generation sequencers.

    This course aims to provide a hands-on introduction to bioinformatics for next generation sequencing and to equip participants with the essential informatics skills and knowledge required to begin analysing next generation sequencing data and carry out some of the most common types of analysis.

    What will I learn?

    The course programme will start with an overview of prominent sequencing technologies and algorithmic theory and principles of bioinformatics, followed by intensive practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis (QC, alignment, assembly, variant calling) to RNA-Seq and data visualisation. Accompanying the lectures and practical sessions will be a series of seminars by invited speakers, who will highlight their cutting-edge work harnessing the power of next generation sequencing technologies to address a wide range of biological questions.

    This course is open to applicants from Africa and is free to attend for non-commercial applicants. Limited bursaries to cover travel, accommodation and sustenance costs are also available. The course will be taught in English.

    The course aims to provide a hands-on introduction to bioinformatics for next generation sequencing, and should not be considered a complete education in the theoretical and mathematical foundations of the topics.

  • Programme

    The hands-on programme will cover several aspects of next generation sequencing data analysis, including lectures, discussions and practical computational sessions* covering the following:

    • Introduction to NGS technologies
    • Introduction to the unix command line
    • Advanced unix for bioinformatics
    • NGS data formats and tools
    • Sequence alignment and QC
    • SNP/indel theory and practical
    • Structural variation theory and practical
    • RNA-seq analysis
    • ChiP-seq analysis
    • Sequencing data visualisation with the Integrated Genomics Viewer (IGV)
    • Accessing public sequencing repositories
    • Participant projects and presentations (final day)

     

    Learning Outcomes
    On completion of the course, participants should be able to:

    • Use the unix command-line as a tool for data analysis
    • Describe the different NGS data file formats available
    • Perform QC assessment of high throughput sequencing data
    • Explain the algorithmic concepts behind short read alignment, variant calling and structural variant detection
    • Perform read alignment, variant calling and structural variation detection using standard tools
    • Analyse RNA-Seq and CHiP-seq data
    • Perform a genome assembly using NGS data
    • Describe the different data types available in public sequence repositories and how they are organised

     

    *Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some familiarity with the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:
    http://www.ee.surrey.ac.uk/Teaching/Unix
    http://swcarpentry.github.io/shell-novice/

  • Instructors and speakers

    Course instructors

    Shaun Aron University of Witwatersrand, South Africa
    Gerrit Botha University of Cape Town, South Africa
    Amel Ghouila Institute Pasteur, Tunisia
    Fatma Guerfali Institute Pasteur, Tunisia
    Petr Danecek Wellcome Sanger Institute, UK
    Jacqueline Keane Wellcome Sanger Institute, UK
    Thomas Keane European Bioinfromatics Institute, UK
    Phelelani Mpangase University of Witwatersrand, South Africa
    Victoria Offord, Wellcome Sanger Institute, UK
    Sumir Panji University of Cape Town, South Africa

  • Cost and bursaries

    Cost

    The course is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and is free to attend for non-commercial applicants.
    Please contact us for the commercial fee.

    Bursaries

    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. If you would like to apply for a bursary, please complete the bursary section of the online application form.

    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.

    Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

  • How to apply

    Prerequisites

    This course is open to applicants from Africa. Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving next generation sequencing data analysis. The course will be taught in English.

    Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some familiarity with the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:
    http://www.ee.surrey.ac.uk/Teaching/Unix
    http://swcarpentry.github.io/shell-novice/

    How to Apply
    Please complete the online application form. Places are limited and will be awarded on merit. 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, line manager 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.