Topic outline

  • General

    Introduction to Next Generation Sequencing

    Bern, 7-8 September 2015

    Organiser(s): Walid Gharib
    Coordinator: Diana Marek
    Trainer(s): Walid Gharib
    Cancellation deadline: September 2015
    Keywords: NGS, genomics, sequencing, bowtie
    Venue: Hochschulstrasse 4 - Seminarraum Nr. 331, Hauptgebäude, University of Bern
    ECTS: 0.5
    Fee: 50 CHF for academics. Others, please contact us



    Usage of NGS is increasing in several biological fields due to a very rapid decrease in cost. However, it often results in hundreds of Gbs of data making the downstream analysis very challenging and requires bioinformatics skills.

    In this module, we will introduce the most used sequencing technologies and explain their decryption concepts.

    We will also introduce the repositories e.g. The European Nucleotide Archive (ENA), Sequence Read Archive (SRA) from which you could retrieve raw data based on specific experiments. We will practice the usage of command line tools to search and fetch NGS raw data in a powerful way.

    Finally, based on different datasets, we will practice screening for quality control and trimming and clipping reads for better downstream analysis. 



    This course is intended to life scientists dealing with NGS technologies.



    Knowledge / competencies:

    • Basic understanding of working with command line tools on Linux or Windows-based operating systems. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module


    • Please bring your own computer with WIFI Eduroam activated
    • You will need to install a Virtual Machine (an emulation of a Linux operating system) on your computer to follow the practicals (see below)
    • Complete the exercise 'UNIX evalutation' at least 4 days before the course - see below


    Learning Objectives

    At the end of the course you should be able to:

    • understand all steps necessary for NGS data analysis
    • run all software used in advanced mode
    • perform a NGS data analysis



    The registration fees for academics are 50 CHF. Participants from non-academic institutions should contact us before application.

    The course is not open

    Deadline for registration and free-of-charge cancellation is set to September 1. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available at

    You will be informed by email of your registration confirmation.


    Additional information

    We will recommend 0.5 ECTS credits for this course (given a passed exam (optional) at the end of the session). 

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    For more information, please contact