DNA Sequence - image by Kate WhitleyThis course type is computational

Next Generation Sequencing Bioinformatics (Remote Classrooms – Africa)

13 April - 10 June 2021Virtual remote classrooms
Deadlines (at 23:59 UTC):
  • Applications to host a classroom Closed

Applications for classroom participants will open shortly.

Learn how to analyse NGS data using the latest bioinformatics tools and resources

  • Course Summary

    In collaboration with H3ABionet, we are pleased to announce our new 2021 Next Generation Sequencing Bioinformtics Remote Classrooms course in Africa.

    This course will apply a blended learning format consisting of locally coordinated classrooms referred to as “remote classrooms”. Click here for more information. Please note: Due to the COVID-19 pandemic, the local classrooms for this course will run virtually, using Zoom and downloadable virtual machines.

    Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential informatics skills required to begin analysing NGS data and apply some of the most commonly used tools and resources for sequence data analysis. 

    The programme will cover prominent sequencing technologies, 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. A variety of applications will be covered from post-sequencing analysis – QC, alignment, assembly, variant calling, RNA-Seq and ChIP-Seq.

    Target audience: The course is aimed at postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals based in Africa who are 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 experience 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/

  • Programme

    The course will run for 8 weeks on Tuesdays and Thursdays from the 13th of April until the 10th of June 2021

    The programme will cover the following topics:

    • Intro to Unix/Linux & running workflows
    • Introduction to NGS Technologies
    • NGS data pre-processing and QC
    • Alignment to reference sequences
    • Variant calling and annotation
    • ChIP-Seq
    • RNA-Seq
    • Genome assembly

    Learning outcomes
    On completion of the course, participants should expect to 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

  • Instructors and speakers

    Course instructors

    Amel Ghouila

    Amel Ghouila
    Bill & Melinda Gates Foundation, USA

    Eugene Gardner

    Eugene Gardner
    Wellcome Sanger Institute, UK

    Fatma Guerfali

    Fatma Guerfali
    Institut Pasteur de Tunis, Tunisia

    Gerrit Botha

    Gerrit Botha
    University of Cape Town, South Africa

    Narendar Kumar

    Narendar Kumar
    Wellcome Sanger Institute, UK

    Petr Daněček

    Petr Daněček
    Wellcome Sanger Institute, UK

    Phelelani Mpangase

    Phelelani Mpangase
    University of the Witwatersrand, South Africa

    Shaun Aron

    Shaun Aron
    University of the Witwatersrand, South Africa

    Sumir Panji

    Sumir Panji
    University of Cape Town, South Africa

    Victoria Offord

    Victoria Offord
    Wellcome Sanger Institute, UK

    Vivek Iyer

    Vivek Iyer
    Wellcome Sanger Institute, UK

  • How to apply

    How to Apply
    Please note
    that applications to HOST a virtual classroom are now closed. Applications for classroom participants will be invited shortly.

    Prerequisites:
    The course is aimed at postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals based in Africa who are actively engaged in or soon to commence research involving next generation sequencing data analysis.

    Priority will be given to applicants who:

    1) currently or will soon have NGS experimental data to analyse
    2) will utilise the bioinformatics techniques taught in at least two of the modules/topic areas listed in the programme outline in their experiments
    3) have a clear plan/opportunity to disseminate the knowledge amongst their peers. We encourage applicants to highlight these areas in their application.

    The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous experience 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:

     

     

In collaboration with:
  1. Logo for H3Abionet
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