Section outline

  • 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