Topic outline

  • General

    Next Generation Sequencing (NGS) methods for identification of mutations and large structural variants

    Lausanne, 11-12 March 2014


    This international event covers several aspects of the identification of genomic structural variants using NGS data. The mini symposium (Day 1) will present the latest developments in the field and the workshop (Day 2) will allow participants to get used to the tools with a virtual machine (VM) prepared during a test case hackathon (see TC2 hackathon session 1 and session 2). Particular emphasis will be given to the comparison of the different analysis tools and the combination of their respective results.

    The ALLBIO ( FP7 CA aims to bring biologists and bioinformaticians together for the effective exploitation of high-throughput data. The focus being to transfer the human genome bioinformatics analysis methods in other genome analysis fields like microbial, plant, and lifestock.
    ALLBIO is the main sponsor of this event, in addition 10 seats of the workshop are sponsored by the COST Action SeqAhead (



    The objective of the mini-symposium is to provide an overview of the existing tools / pipelines available for NGS analysis, as well as to present some data using those tools. The objective of the workshop is to allow participants using the pipeline, either with our data, or with their own data.

    Requirements for the workshop

    - Basic knowledge of UNIX (explore SIB's UNIX Fundamentals e-learning module here)

    - Laptop with at least 4 GB RAM, 50 GB free disk space, WIFI and VirtualBox preinstalled


    Applications are closed.

    Additional information



  • Programme

    Tuesday March 11: Mini symposium

    Genopode building, auditorium A

    Welcome address

    Dr. Tiffanie Yael Maoz (Moss)

    Weizmann Institute of Science, Rehovot, Israel
    The New Face of SV Detection and Tool Development

    Prof. Alexandre Reymond

    Center for Integrative Genomics, University of Lausanne, Switzerland
    Large rare variants have a significant burden in general populations

    Coffee break

    Dr. Tobias Rausch

    EMBL Heidelberg, Germany
    Population-based structural variant calling using Delly

    Prof. Bart Deplancke

    Laboratory of Systems Biology and Genetics, EPFL / SIB, Lausanne, Switzerland
    Characterizing genomic variation and assessing its impact on gut immunocompetence in a natural Drosophila population


    Dr. Alexander Schoenhuth
    / Dr. Tobias Marschall
    Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
    Discovering and genotyping twilight-zone indels with MATE-CLEVER

    Dr. Valentina Boeva

    Inserm U900 / Institut Curie / Mines ParisTech, France
    Detection of structural and copy number alterations in cancer genomes using different types of sequencing data

    Coffee break

    Mr. Yogesh Paudel

    Wageningen University, The Netherlands
    Copy number variation (CNV) detection method using next generation sequencing (NGS) data

    Prof. Can Alkan

    Bilkent University, Ankara, Turkey
    Characterization of mobile element insertions using NGS

    17:00 Farewell

    Wednesday March 12: Hands-on Workshop

    Genopode building, room 2020

    Analysing structural rearrangement of a genome with Next Generation Sequencing (NGS) data is a difficult task, especially when large insertions and deletions have to be compared to a reference genome. We developed a pipeline to compare the results obtained by various tools and combine them together to a final consensus call. During this workshop we will present our pipeline within a virtual machine (VM) allowing interested researchers to upload their own data in order to detect potential insertions and deletions.

    Organisers: Wai Yi Leung / Hailiang Mei, Sequencing Analysis Support Core, Leiden University Medical Center, NL, Dr. Tiffanie Yael Maoz (Moss) Weizmann Institute of Science, Rehovot, IL, Dr. Alexander Schoenhuth / Dr. Tobias Marschall Centrum Wiskunde & Informatica, Amsterdam, NL, Yogesh Paudel Wageningen University, NL, Dr. Laurent Falquet, University of Fribourg, CH

    (UNIX proficiency is required, as well as a laptop with at least 4 GB RAM, 50 GB free disk space, WIFI and VirtualBox preinstalled)

    9:00 Introduction to the project, SV detection methods, tool selection (Yael, Wai Yi)

    9:30 Introduction to makefiles (Wai Yi)

    10:00 Running the VM and testing it (Wai Yi, Laurent, Tobias, Yogesh, Alex, Yael)

    13:00 Present IGV results (Yael)

    parallel group 1

    14:00 How to load your own data (Wai Yi, Tobias)

    15:00 How to adapt the VM for another software (Wai Yi, Tobias)

    parallel group 2

    14:00 Discussion of projects, current difficulties, issues (Laurent, Yogesh, Alex, Yael)