Topic outline

  • General

    Introduction to Next Generation Sequencing

    Bern, 7-8 September 2015


    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. 



    • 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 containing the software and data needed) on your computer to follow the practicals (see below)
    • Complete the exercise 'UNIX evalutation' at least 4 days before the course - see below


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

    The course is full.

    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.


    Bern, Hochschulstrasse 4 - Seminarraum Nr. 331, Hauptgebäude, University of Bern

    Additional information

    The course will be taught by Walid Gharib.

    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

  • Programme

    Monday 7 September

    Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval  

    9:15 - 9:45 - UNIX reminder
    9:45 - 10:30 - Introduction to technologies and applications (1)

    • Roche 454 - Pyrosequencing
    • llumina - sequencing by synthesis

    10:30 - 11:00 - Coffee Break

    11:30 - 12:15 - Introduction to technologies and applications (2)

    • Pacific Biosciences - SMRT Sequencing
    • Ion Torrent Sequencing - Semiconductor sequencing

    12:15 - 13:30 - Lunch Break

    13:30 - 13:45 - NCBI: E-utilities using Unix command line
    13:45 - 15:00 - E-utilities usage - Practicals

    15:00 - 15:30 - Coffee break

    15:30 - 15:45 - Sequencing archives, SRA, ENA and DDBJ
    15h45 - 17:00 - Fetching sequencing data - Practicals (Combining E-utilities and SRA tools)


    Tuesday 8 September

    File Formats, quality assessment, cutting/trimming/filtering and sequence alignement

    9:00 - 10:00: File formats and Quality controls
    9:45 - 10:30: Interpretation of a Fastqc report and acting upon for cutting/trimming reads

    10:30 - 11:00: Coffee break

    11:00 - 12:15: Quality control - Practicals

    12:15 - 13:30 - Lunch Break

    13:30 - 15:30 - Trimming/filtering quality control - Practicals
    16:00 - 17:00 - Alignment to a reference genome - Small intro and practicals
    17:00 - 17:05 - Two words about the upcoming NGS modules