Topic outline

  • Bioinformatics of long read sequencing - ready for the third generation

    5-6 October 2017, University of Zurich, Irchel Campus

    This page is addressed to registered participants. To access course description, please click here

    For any assistance, please contact training@sib.swiss.

  • Schedule

    Day1    
     Introduction  09:00 Introduction to the current technologies used for long read sequencing - Andrea Patrignani (ETHZ/SIB)
     Mini-symposium 09:45 Methods for clustering highly similar isoforms from targeted PacBio sequencing - Mark Robinson (University of Zurich/SIB)
      10:10  Coffee break
      10:30 Using long read sequencing technologies to improve the study of alternative splicing - Amina Echchiki (University of Lausanne/SIB)
      10:55 The application of third generation, single molecule sequencing to alternative splicing and low frequency variant detection - Giancarlo Russo (ETHZ/SIB)
      11:20 Integrating NGS data for the assembly of prokaryotic genomes & a proteogenomics approach to identify their complete protein-coding potential - Christian Ahrens (Agroscope/SIB)
      11:45 Long read sequencing and assembly - fairytale and reality - Emanuel Schmid-Siegert (SIB)
      12:10 Round table with the speakers
      13:00 Lunch
    Hands-on 14:00-17:30

    Hands on - Amina Echchiki, Walid Gharib, Dan Jeffries and Kamil Jaroň (UniL/UniBern/SIB)

    In this session, the participants will familiarise with the raw long reads, learn how to assemble genomic reads, how to map genomic and RNA-seq reads to a reference genome, and finally how to proceed to transcriptome assembly.

    Day2     
    Hands on  09:00 - 12:30

    Hands on - Amina Echchiki, Walid Gharib, Dan Jeffries and Kamil Jaroň (UniL/UniBern/SIB)

    In this session, participants will interpret assemblies they have computed on the first day, learning how to assess quality of a genome assembley and run dowstream analysis. 

      12:30 Lunch
    Hands on  14:00 - 17:30

    Analysis of PacBio Long Reads using the SMRT Analysis Package and SUSHI - Weihong Qi and Giancarlo Russo (ETHZ/SIB)

    This session consists of lectures providing an overview of the individual pipelines in the SMRT Analysis Package as well as hands-on exercises using the SUSHI data analysis framework developed at FGCZ, including quality control of PacBio data and data preparation, sequence alignment and variant detection, de novo assembly.

     

    • Material

      Here is a link to the full practicals for the RNA-seq and genome assembly (Day 1 and morning of Day 2).