DNA Sequence - image by Kate WhitleyThis course type is computational

Next Generation Sequencing Bioinformatics

01 - 07 December 2019Wellcome Genome Campus, UK
Deadlines (at 23:59 UTC):
  • Application and bursary deadline 12 September 2019
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Essential informatics skills and knowledge to begin analysing next generation sequencing data

  • 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.

    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/

    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.

    Related courses
    Please note that this course is aimed at applicants solely interested in analysis of NGS data. Applicants interested in laboratory-based training in NGS technologies and methodologies should consider our Next Generation Sequencing lab course. Email us to be kept updated on the 2020 NGS lab course.

  • 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
    • Advanced unix
    • 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 advanced unix commands 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 and speakers

    Course instructors

    Jacqueline Keane

    Jacqueline Keane
    Wellcome Sanger Institute, UK

    Thomas Keane

    Thomas Keane
    EMBL-EBI, UK

    Petr Daněček

    Petr Daněček
    Wellcome Sanger Institute, UK

    Victoria Offord

    Victoria Offord
    Wellcome Sanger Institute, UK

    Michael Quail

    Michael Quail
    Wellcome Sanger Institute, UK

    Shane McCarthy

    Shane McCarthy
    Wellcome Sanger Institute, UK

    Vivek Iyer

    Vivek Iyer
    Wellcome Sanger Institute, UK

    Guest speakers

    The course will feature research seminars from distinguished guest speakers. Speakers for the 2019 course will be announced shortly. Previous speakers have included:

    Claire Jenkins Public Health England, UK
    Frank Chan Friedrich Miescher Laboratory, Germany
    Sofia Chen Wellcome Trust Sanger Institute, UK
    Ximena Ibarra-Soria Cancer Research UK Cambridge Institute, UK

  • Cost and bursaries
    Cost Accommodation / meals
    *Course fee £725 This is a residential course and the fee includes all accommodation and meals.

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

    Bursaries

    Limited bursaries are available (up to 50% reduction on 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.

    Where there are many bursary applications, the selection committee may issue smaller amounts.

    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.

    Additional funding opportunities
    Visit our support page for additional financial support currently available.


    Accommodation services phishing scam – please be vigilant. More information.

  • 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.

    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.

    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/

    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.

    How to Apply
    Please click the Apply button above to begin the online application process. 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.

    Travel visas
    Successful applicants will be provided with a support letter for their visa application, if required.

    Please visit the following websites for further information on visiting the UK:

  • Testimonials

    Feedback from the 2018 course:

    “The course was superbly organised and very well delivered. A great balance between theory and practicals.”

    “This course has been an amazing experience and I consider my participation a highly valued gift. The people I have met, the instructors and their warm, friendly, enthusiastic approach and brilliant performance has left me with inspiration for futher work with bioinformatics.”

    “I really enjoyed the course, thoroughly enjoyable. The course exceeded my expectations. I found it very useful in terms of the command line and how to use bioinformatic tools to analyse my data. Jacqui & Thomas and all the instructors were very accessable and the activities the sessions were
    very interactive and informative.”

    “I would just like to say thank you for all the excellent teaching I received.”

    “I have enjoyed the course and learnt a lot. It has really showed me how well such a course can be run and how much participants gain from this.”

    “Thank you it was amazingly organized and executed!”