DNA Sequence - image by Kate WhitleyThis course type is computational

Next Generation Sequencing Bioinformatics (Bandar Sunway, Malaysia)

09 - 14 February 2020
Deadlines (at 23:59 UTC):
  • Application and bursary deadline Closed

Learn to analyse next generation sequence data to address a wide range of biological questions

  • Summary

    Summary

    In collaboration with the Monash University Malaysia Genomics Facility (MUMGF), we are delighted to offer this free to attend course on application of bioinformatics tools and resources in the analysis of next generation sequence data.

    High throughput sequencing has gained widespread adoption as an essential experimental assay for biological research. Analysing high throughput sequencing data involves an array of different bioinformatics tools and techniques. Therefore, it is important for experimental scientists to have the bioinformatics skills required to effectively assess and analyse data produced by next generation sequencing.

    This course aims to provide a hands-on introduction to bioinformatics for next generation sequencing and 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.

    What will I learn?

    The course programme will start with a history and overview of sequencing technologies and algorithmic theory and principles of bioinformatics, followed by intensive practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis (QC, alignment, assembly, variant calling) to RNA-Seq and data visualisation. Accompanying the lectures and practical sessions will be a series of seminars by invited speakers, who will highlight their cutting-edge work harnessing the power of next generation sequencing technologies to address a wide range of biological questions.

    This week-long course is open to applicants from Asia and is free to attend for non-commercial applicants. Limited bursaries to cover travel, accommodation and sustenance costs are also available. The course will be taught in English.

    *Please note:
    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.

  • 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
    • Introduction to the unix command line
    • NGS data formats and tools
    • Sequence alignment and 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 (IGV)
    • Accessing public sequencing repositories
    • Genome assembly theory and practical
    • Participant projects and presentations (final day)

     

    Learning Outcomes
    On completion of the course, participants should be able to:

    • Use the unix command-line as a tool for data analysis
    • Describe the different NGS data file formats available
    • Perform QC assessment of high throughput sequencing data
    • Explain the algorithmic concepts behind read alignment, variant calling and structural variant detection
    • Perform read alignment, variant calling and structural variation detection using standard tools
    • Analyse RNA-Seq and CHiP-seq data
    • Perform a genome assembly using NGS data
    • Describe the different data types available in public sequence repositories and how they are organised

     

    *Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some familiarity with 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/

  • Instructors and speakers

    Lead Organisers/Instructors

    Jacqueline Keane

    Jacqueline Keane
    Wellcome Sanger Institute, UK

    Thomas Keane

    Thomas Keane
    European Bioinfromatics Institute, UK

    Qasim Ayub

    Qasim Ayub
    Monash University, Malaysia

    Instructors and Assistants

    Farhang Aghakhanian

    Farhang Aghakhanian
    Monash University, Malaysia

    Petr Daněček

    Petr Daněček
    Wellcome Sanger Institute

    Jasbir Kaur Dhaliwal

    Jasbir Kaur Dhaliwal
    Monash University, Malaysia

    Victoria Offord

    Victoria Offord
    Wellcome Sanger Institute

    Wee Wei Yee

    Wee Wei Yee
    Monash University, Malaysia

    Swaine Chen

    Swaine Chen
    Genome Institute of Singapore

    Nirmala Arul Rayan

    Nirmala Arul Rayan
    Genome Institute of Singapore

    Adaikalavan Ramasamy

    Adaikalavan Ramasamy
    Genome Institute of Singapore

  • Cost and bursaries

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

    Bursaries
    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. If you would like to apply for a bursary, please complete the bursary section of the online application form.

    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. Priority will be given to applicants from low- and middle-income countries.


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

  • How to apply

    Prerequisites
    This course is open to applicants from Asia. 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. The course will be taught in English.

    *Please note: The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some familiarity with 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/

    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.

  • Testimonials

    Feedback from the 2019 Overseas NGS Bioinformatics courses:

    “I appreciate the excellent the organizers and instructors, and I will recommend this course because I think that it applied a excellent method of teaching, which is learning by doing”.

    “I thank you for being selected for the course and have the opportunity to learn about the NGS bioinformatics analysis and meet people from all over Latin America who work in the same area as me”.

    “I have benefitted tremendously from this course. I am now able to perform some bioinformatics analyses on my sequencing reads and also provide some basic level of guidance to my colleagues”.

    “The first day of networking and getting to know everyone was very helpful in breaking
    the ice and getting comfortable”.

    “I definitely enjoyed the real hands-on practical work, with necessary and sufficient time allocated
    for it, and that we had more than enough instructors that could assist us”. 

    “The best thing about this course was focus given to practicals, the experience and knowledge of
    the instructors, and the number and diversity of instructors”.