Topic outline

  • General

    De novo genome assembly workshop

    Lausanne, 6 May 2011


    Next generation Sequencing technologies deliver huge amounts of short sequences for a relative low price. The data is frequently of low quality (noise and artifacts) and must be cleaned before usage; the assembly steps are often difficult due to the nature of the sequences (repeats, GC content), the quality of the tools and can be very different with a reference (by mapping) or without a reference (de novo). The final results must be evaluated with various criteria. The aim of the course are: (i) learn how to measure the quality of the data, clean and extract the good information. (ii) learn to assemble a genome de novo (without a reference) (e.g., SOAPdenovo, ABySS, Velvet).

    Important note:

    The mapping of reads onto a known reference will be given in a separate workshop (e.g., MAQ, Bowtie, BWA).

    Objectives:

    • Discover the type of data generated by NGS technologies
    • Quality Control and cleaning of the data
    • Learn how to use Vital-IT's computing cluster for de novo genome assembly
    • Tips and tricks for effective and efficient assembly
    • Discuss particular needs and requirements of course participants

    Requirements:

    Basic understanding of working with UNIX command line tools on Linux or MacOSX

    Practical organization - Location

    Sessions runs from 9:00 to 17:00 approximately, with a lunch break.
    This one-day course is held at the Génopode building (Auditorium B) of the University of Lausanne.

    Registration:

    The course is currently full and the registration is closed.
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