Topic outline

  • General

    NGS - Quality control, Alignment, Visualisation

    4 - 6 November 2020

    room 304 and 028. OG West, Universit├Ąt 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 Geert van Geest, for any assistance, please contact training@sib.swiss.

    • Programme

      4 November

      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)


      5 November


      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


      6 November

      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.