This course type is laboratory

Next Generation Sequencing

13 - 20 April 2018Wellcome 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- and computer–based course is directed
    at scientists who will be generating and interpreting sequence
    information and wish to gain a better understanding of the techniques
    involved and their applications.

    Taught by instructors from the prestigious Wellcome Trust Sanger
    Institute, the course will include theoretical and hands-on practical
    training on current and emerging next-generation sequencing systems,
    including,

    • PacBio
    • Illumina Miseq/HiSeq
    • Oxford Nanopore MinION

    The aim of the course is to allow participants to make informed decisions
    about which technologies and methodologies to apply to solve specific
    research questions they may face in the future. A variety of applications
    will be covered, e.g., RNA-Seq, target enrichment, bacterial sequencing,
    cancer genomics, human variation analysis, etc. All the basic techniques
    of post-sequencing analysis will also be covered (QC, alignment,
    assembly, variant calling, etc.).

    Feedback from the 2017 course

    “This very intensive course provides a comprehensive technology
    spanning overview of the NGS technology: including library preparation,
    introduction in several NGS platforms and detailed data analysis,
    starting with LINUX introduction. I have not found any comparable other
    course and I am glad to have had the opportunity to take part in it.”

    “Thank you to all involved in the course. It was intense but overall a
    truly fantastic experience where I learned many new skills and created
    lots of new friends.”
    “The Next Generation Sequencing Course 2017 helped me to stick the
    laboratory side together with the bioinformatics site and helped to close
    my knowledge gaps in the NGS data analysis!”
    “I would like to thank everybody from the organising team of Advanced
    courses to the instructors for such a wonderful,
    life-time experience! I gained a lot from this course and for sure the
    knowledge will help me advance to the next level of my project.”
    “This was a really well conducted course and I go back with a much
    greater understanding of NGS and its different aspects. Thanks to the
    whole advanced courses team for making this such a great
    experience!”

  • 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
      problems

    Learning Outcomes
    By the end of this course participants will be able to:

    • make high quality libraries for Next Generation Sequencing
    • explain and evaluate a range of sequencing technologies, current and future (3rd generation) platforms
    • demonstrate how to set up a sequencing run
    • critically assess a sequencing run

    *Linux experience
    This course includes several data
    analysis modules using the Linux-based
    operating system. 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)

    There are numerous online introductory tutorials to the UNIX/Linux
    operating system and commad line, including:
    http://rik.smith-unna.com/command_line_bootcamp
    http://www.ee.surrey.ac.uk/Teaching/Unix
    http://swcarpentry.github.io/shell-novice/

  • Instructors / Speakers

    Course instructors
    Tony Cox Wellcome Trust Sanger Institute, UK
    Michael Quail Wellcome Trust Sanger Institute, UK
    Jacqui Keane Wellcome Trust Sanger Institute, UK

    Guest speakers
    Daniel Gaffney Wellcome Trust Sanger Institute, UK
    Elizabeth Murchison University of Cambridge, 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. Please also review
    the Linux experience information under the Programme
    tab.

    Applications
    Applications can be submitted online. 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.

    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 only 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 the fee is £1065, including all
    accommodation and meals. This subsidised fee is available to all
    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 a 50% reduction 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.