Topic outline

  • General

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    Introduction to Next Generation Sequencing

    17-18 May 2016

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

    Tuesday 17 May

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

    9:15 - 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)

     

    Wednesday 18 May

    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

  • Virtual machine

    Before the beginning of the course, you will need to have an emulation of a linux OS (virtual machine) on your computer to be able to access all the data and software you will use during the practicals.

    To this end, you first need to have virtualbox installed on your computer. Please download and install the latest version.

    Then download the virtual image (.ova) here (time consuming almost 6.5 GB) and import it into virtualbox (it might take few minutes). Then start the virtual image to check it works on your computer (password: user-SIB).

    If at the end of the procedure, you are still not able to run the virtual machine, please contact us sufficiently in advance at training@sib.swiss as no technical problem with the virtual machine will be handled during the course.

    Please also note that you need a computer with minimum of 4 GB memory. The virtual machine itself requires 3 GB memory. And at least 30 GB free space on your hard disk.