This course type is laboratory

Next Generation Sequencing

11 - 17 March 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    Next-generation sequencing has become the premier tool in genetic and
    genomic analysis. This laboratory-based course is directed at scientists
    who will be generating and interpreting sequence information in their
    research and wish to gain a better understanding of the techniques
    involved and their applications. This course is not meant to replace the
    manufacturers’ training normally supplied with new instruments, nor is it
    intended to be a training course for those solely interested in
    next-generation sequencing bioinformatics.

    The course will include theoretical and practical information on all of
    the next-generation sequencing systems available and those on the near
    horizon. The laboratory element will cover a mix of technologies that
    will be determined nearer the time, but will be chosen from platforms
    including, PacBio, Illumina Miseq/HiSeq and Oxford Nanopore MinION. One
    aim of the course is to allow participants to make informed decisions
    about which technology to apply to solve specific research questions they
    may face in the future. A variety of applications will be covered as time
    permits, e.g., RNA-Seq, target enrichment, bacterial sequencing, cancer
    genomics, human variation analysis, etc. All the basic techniques of
    post-sequencing analysis will be covered, QC, alignment, assembly,
    variant calling, etc.

    Please note: For the data analysis components of the
    course, applicants will require a working knowledge of the Linux
    operating system. This can be obtained by various methods and will be
    enforced.

    Feedback from the 2015 course
    “The quality and standard of this course was excellent in every
    aspect.”
    “I would like to say that strongly recommend this course based on the
    quality, structure and working conditions offered; as well as the
    knowledge, availability and good mood coordinators and instructors.”

    “Generally, the course was great. -Lecture discussions complemented the
    lab very well. -Lecturers/Instructors were very competent and
    accommodating.”

  • Programme

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

    Library Prep

    • Making libraries from samples
    • Both theory and practical sessions

    Sequencing

    • Overview: Motivation and fundamental concepts
    • Detailed description of prominent sequencing technologies: current and future (3rd generation) platforms
    • Hands-on laboratory work: preparing chips for sequencing and performing sequencing runs on various platforms

    Data analysis

    • Data QC: How to determine if a run has performed well
    • Alignment to a reference, de-novo assembly, SNP and structural variant-calling of next generation DNA and RNA data
    • IT and the data storage problem


    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.

  • Instructors / Speakers

    Course instructors
    Tony Cox Wellcome Trust Sanger Institute, Hinxton, UK

    Michael Quail Wellcome Trust Sanger Institute, Hinxton,
    UK

    Guest speakers
    Julian Parkhill Wellcome Trust Sanger Institute, UK

    Elizabeth Murchison Wellcome Trust Sanger Institute, UK

  • How to Apply

    Prerequisites
    Applicants should be postdoctoral scientists, senior PhD students or
    junior faculty members actively engaged in or soon to commence research
    involving next generation sequencing instrumentation.

    Linux experience
    This course includes a substantial element of sequence data QC and
    analysis performed on Linux-based computers. To benefit fully from the
    course it is essential that successful applicants are comfortable working
    in a Linux-based environment prior to the course. In particular,
    applicants will be expected to use the command line terminal interface.

    Applicants will need to be familiar with, and able to perform, the
    following:
    creating, copying, moving and deleting text files and directories,
    modifying file and directory permissions, navigating directory
    structures, examining the contents of text files, executing programs from
    the command line using pipes and output redirection, compressing and
    decompressing files (using zip or gzip)

    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 £1020 towards board and lodging for non-commercial
    applicants. Please contact us for the commercial fee.

    Applications
    Applications for this course can now 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
    Advanced Courses are subsidised for non-commercial applicants from anywhere in the world. 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.