Topic outline

  • General

    NGS - Quality control, Alignment, Visualisation

    12 - 14 June 2019

    room 304 / 3. OG West, Universität Bern, Hochschulstrasse 4 (main building of the University of Bern).

    This page is addressed to registered participants. To access course description and application form, please click here.

    This course will be taught by Walid Gharib, for any assistance, please contact training@sib.swiss.

  • Programme

    12 June

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

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

    • Ion Torrent Sequencing - Semiconductor sequencing
    • llumina - sequencing by synthesis

    10:30 - 11:00 - Coffee Break

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

    • Pacific Biosciences - SMRT Sequencing
    • Oxford Nanopores - MinIon, GridIon

    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)


    13 June


    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

                            - Trimming/filtering quality control - Practicals

    12:15 - 13:30 - Lunch Break

    13:30 - 15:30 -  Alignment to a reference genome - Small intro and practicals
    15h30 - 17:00 -  Sorting, Indexing the alignment and quick visualization using IGV genome viewer


    14 June

    9:00 - 10:30: Visualisation using IGV lecture 
    10:30 - 11:00: Coffee break

    11:00 - 12:15:  Practicals using cancer variants dataset

    12:15 - 13:30: Lunch Break

    13:30 - 15:30: Practicals using RNAseq and CHIPseq datasets

    15h30 - 17:00: useful tips and tricks in NGS/concluding remarks


    END

    • Prerequisites

      Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.

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