Topic outline

  • General

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

    Lausanne, 11-12 March 2014

    Overview

    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 (http://www.allbioinformatics.eu) 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 (http://www.seqahead.eu).

      

    Objectives

    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

    Application

    Applications are closed.

    Additional information

    Location

    Contact: training@isb-sib.ch

    • Programme

      Tuesday March 11: Mini symposium

      Genopode building, auditorium A

      9:00
      Welcome address

      9:10-9:50
      Dr. Tiffanie Yael Maoz (Moss)
      Weizmann Institute of Science, Rehovot, Israel
      The New Face of SV Detection and Tool Development

      9:50-10:30
      Prof. Alexandre Reymond
      Center for Integrative Genomics, University of Lausanne, Switzerland
      Large rare variants have a significant burden in general populations

      10:30-11:00
      Coffee break

      11:00-11:40
      Dr. Tobias Rausch
      EMBL Heidelberg, Germany
      Population-based structural variant calling using Delly

      11:40-12:20
      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

      12:20-13:40
      Lunch

      13:40-14:20
      Dr. Alexander Schoenhuth       / Dr. Tobias Marschall
      Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
      Discovering and genotyping twilight-zone indels with MATE-CLEVER

      14:20-15:00
      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

      15:00-15:30
      Coffee break


      15:30-16:10
      Mr. Yogesh Paudel
      Wageningen University, The Netherlands
      Copy number variation (CNV) detection method using next generation sequencing (NGS) data

      16:10-16:50
      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)