Section outline

  • 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