This course type is computational

Next Generation Sequencing Bioinformatics

01 - 07 October 2017Wellcome 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 course 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.

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

    • 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: 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. 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 2017 lab course can be found
    here and is next scheduled for April 2018.
    Email us
    for updates
    .

    Feedback from the 2016 Next Generation Sequencing Bioinformatics
    course

    • Excellent course, highly recommended to anyone interested in bioinformatics whether they have some knowledge or want to start analysing their own data. Wonderful instructors and selection of participants and instructors. Very thankful that the opportunity was given to me.
    • I enjoied the course very much. I am going to use many of the techniques that I have learned in my research.
    • I would like to thank everyone involved in organization of the course! Well done! And I wish you keep it at the same great level and spread knowledge in this friendly atmosphere.
    • Thank you so much for the wonderful week, it opened a new world for me.
    • Thank you so much for everything! It was a life changing experience for me!
  • 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
    • 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 acquired:

    • 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 lead instructors
    Thomas
    Keane
    EMBL-European Bioinformatics Institute, UK
    Jacqui
    Keane
    Wellcome Trust Sanger Institute, UK

    Guest speakers
    Kate Baker University of Liverpool, UK
    Gosia Trynka Wellcome Trust Sanger
    Institute, UK
    Steven Munger The Jackson Laboratory, USA
    Alejandro Sanchez-Flores National
    Autonomous University of Mexico

  • How to Apply

    Prerequisites
    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.

    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 £680 towards
    board and lodging for non-commercial applicants. Please contact us for
    the commercial fee.

    Additional limited bursaries are available (up to 50%
    of the course fee)
    and are awarded on merit. Please see the “Bursaries”
    tab for details.

    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

    Travel visas
    Please contact the
    event organiser if you require a letter to support a travel visa
    application. Note that letters will be provided to confirmed attendees.

    Non-European Economic Area or Swiss nationals may be required to have a
    visa to enter the UK.
    Early application is strongly advised, as this process can take 6-8 weeks
    or longer.

    Please visit the following websites for further information:
    UK Border Agency website and information for general visitors and business
    visitors.

  • Cost / Bursaries

    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 £680 towards board and lodging for
    non-commercial applicants. Please contact us for the commercial fee.

    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.