Topic outline

  • General

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    NGS genome & transcriptome assembly and analysis

    Fribourg, June 16-18 2014 + June 20 Mini-symposium BEFRI Genomics Day

    Overview

    This three-days practical course will detail Next Generation Sequencing (NGS) methodologies and how to analyse the sequence data to assemble de novo genomes or transcriptomes. Three main chapters will be covered both theoretically and in practice: 

    a) Techniques and UNIX tutorial
    b) Genome de novo assembly and calling SNPs by remapping
    c) Transcriptome denovo assembly and exons calling via remapping

    An extra day (20 June) will be dedicated to mini-symposium jointly organized by the Universities of Bern and Fribourg.

    Objectives

    The participants will learn how to perform quality control, trimming/filtering, and how to assemble short reads with various available software tools. They will also learn how to compare assemblies and how to annotate rapidly their draft assemblies. 

    Requirements 

    UNIX command-line basic knowledge is required. Participants are asked to pass the UNIX Fundamentals self-learning module.
    For the exercices, participants should bring their own laptops with at least 4Gb RAM and WIFI capable.

    Please install VirtualBox software for your laptop: https://www.virtualbox.org

    We will provide the Virtual Machine with all the required software.

    Application

    Application is now closed (the course is full).

    Please note that the number of seats is limited to 25 and that the priority will be given to PhD students members of StarOmics doctoral program.
    Deadline for registration and cancellation is set to the 31st of May 2014.

    Practical organization - Location and schedule

    • Université de Fribourg
    • Building PER-04 seminar room O.109 and auditorium O.110 (Plant Biology)

    You can reach it (stop "Charmettes") by bus Nr 1, 3 or 7 from the train station (5min) or by walking (15min).

    Sessions runs from 9:15 to 17:00 approximately, with a lunch break.

    Additional information

    We will recommend 1 ECTS credits for this course (given a passed exam that will consist in a skills assessment during the practicals).

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    For administrative questions, please contact staromics@cuso.ch
    For technical and scientific questions, please contact training@isb-sib.ch

  • Monday, June 16, 2014

    9:15 Introduction to the sequencing methods (Sylvain Pradervand, GTF, UniL).

    11:00 Introduction to UNIX and HPC, installation of VM (Laurent Falquet, UniFr).

    13:30 Quality Control, trimming, filtering (Sylvain Pradervand, GTF, UniL).

  • Tuesday, June 17, 2014

    9:15 De novo Genome Assembly and Annotation (Laurent Falquet, UniFr)

    13:30 Remapping on a reference genome, SNP and Variants calling (Vidhya Jagannathan, UniBe)

  • Wednesday, June 18, 2014

    9:15 Transcriptome denovo assembly and comparison (Gina Cannarozzi, UniBe)

    13:30 Remapping RNAseq reads on a genome, transcript reconstruction and alternative exon identification (Thierry Sengstag, UniBas). 

  • Friday, June 20, 2014: Mini-symposium BEFRI Genomics Day

    Program

    Mini-symposium application is now open.