This course type is computational

Next Generation Sequencing Bioinformatics

23 - 29 October 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    Next generation sequencing has become an essential tool in 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 next generation sequencing bioinformatics course aims 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.

    The programme will cover the algorithmic theory and principles of
    bioinformatics, with a strong focus on practical computational sessions
    using sequence analysis techniques and tools applicable to any species or
    genome size. Accompanying the lecture and practical sessions will be a
    series of seminars by invited speakers, who will highlight their
    ground-breaking work in applications of next generation sequencing.

    Please note: The practical sessions will be taught
    exclusively through Unix/Linux. Therefore, participants are required to
    have some previous exposure of using the Linux operating system. This
    will be essential for participants to fully benefit from the course. 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.

    Learning Outcomes
    On completion of the course, participants can expect to have:

    • A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
    • Knowledge of how to do QC assessment of high throughput sequencing data
    • Understanding of the algorithmic concepts behind short read alignment and variant calling, and practical experience using the software
    • Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
    • Knowledge of the organisation and sequencing data types available in public sequencing repositories

    Please note: This course is aimed at applicants solely
    interested in analysis of NGS data. Applicants interested in practical,
    laboratory-based training in NGS technologies and methodologies should
    consider our Next Generation Sequencing lab course. Details of
    the 2016 lab course can be found here and is next scheduled for March
    2017. Email
    us
    for updates.


    Feedback from the 2015 Next Generation Sequencing Bioinformatics
    course

    -Thank you for putting on such a wonderful course! I had a fantastic
    time and recommend this course to all of my colleagues. I appreciated how
    kind and patient all of the instructors were in teaching us what must be
    second nature to them, particularly when it comes to using command line.
    Thank you again!
    -Greatly appreciate the effort done by all the course team; organizers,
    instructors and WGC advanced courses staff members. All are professional,
    helpful and dedicated to do the best. Thank you!
    -The organizers and instructors were brilliant, incredibly patient and
    generous with their time.
    -Thank you so much for a wonderful week! So excited to get our data back
    and be ready to jump into the analysis!
    -I would just like to personally thank Thomas and Jacqui Keane for all
    their hard work organising such a wonderful course. I learnt so much,
    really enjoyed myself, made some great contacts and am now excited to put
    my NGS bioinformatics skills to use. In addition, I’d like to thank all
    the module leaders for their hard work and for delivering such excellent
    modules. Finally, please pass on my thanks to those that are not named
    module leaders but were the helpers (PhD students, bioinformaticians,
    Postdocs etc) who were around during the practical sessions – they were
    so patient and helpful answering my (almost) constant questions – thank
    you so much!

  • 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 and tour of Sanger Institute facilities
    • Introduction to the unix command line
    • Introduction to scripting for bioinformatics
    • NGS data formats and tools
    • Sequence alignment+QC
    • SNP/indel theory and practical
    • Structural variation theory and practical
    • De novo sequence assembly
    • RNA-seq analysis
    • ChiP-seq analysis
    • Sequencing data visualisation with the Integrated Genomics Viewer
    • Accessing public sequencing repositories
    • Participant projects and presentations (final day)

    Learning Outcomes
    On completion of the course, participants can expect to have:

    • A working knowledge of the unix command-line and writing basic shell scripts for automating bioinformatics tasks
    • Knowledge of how to do QC assessment of high throughput sequencing data
    • Understanding
      of the algorithmic concepts behind short read alignment and variant
      calling, and practical experience using the software
    • Experience analysing RNA-Seq and CHiP-seq data for measuring abundance
    • Knowledge of the organisation and sequencing data types available in public sequencing repositories
  • Instructors / Speakers

    Course instructors
    Thomas Keane Wellcome Trust Sanger Institute, UK
    Jacqui Keane Wellcome Trust Sanger Institute, UK

    Guest speakers
    Mary O’Connell University of Leeds, UK
    Clare Smith University of Massachusetts Medical School, USA
    Aylwyn Scally University of Cambridge, UK
    Stephen Bentley Wellcome Trust Sanger Institute, UK

  • How to Apply

    Target audience and prerequisites
    Applicants should be postdoctoral scientists, senior PhD students, junior
    faculty members or clinicians actively engaged in or soon to commence
    research involving next generation sequencing data analysis.

    Linux experience:
    The practical sessions will
    be taught
    exclusively through Unix/Linux. Therefore, participants are
    required to
    have some previous exposure of using the Linux operating
    system. This
    will be essential for participants to fully benefit from
    the course.


    Cost

    The
    course is subsidised by the Wellcome Genome Campus Advanced Courses
    and Scientific Conferences Programme. This is a residential
    course and
    there is a fee of £665 towards board and lodging 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
    Deadline for Applications: Closed

  • Bursaries

    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
    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.