Section outline

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    Bioinformatics of long read sequencing

    8-9 November 2018, 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

    Thursday 08 November 2018

    Mini-symposium
    Introduction 09:00 Introduction to the current technologies used for long read sequencing - Andrea Patrignani (ETHZ and SIB)
    09:45 Reference-based gene expression analysis with long-read sequencing data - Charlotte Soneson (University of Zurich, FMI and SIB)
    10:10 Coffee break
    10:30 Improving protein-coding gene calls using a long-reads based genome assembly - Amina Echchiki (University of Lausanne and SIB)
    10:55 Applications of single molecule sequencing: alternative splicing, rare variants and methylation - Giancarlo Russo (ETHZ and 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 and SIB)
    11:45 Studying Bacterial gene flow in real time; The benefits of using long reads data - Marc Garcia Garcera (University of Lausanne and SIB)
    12:10 Round table with the speakers
    13:00 Lunch

    End of the minisymposium

    Hands-on 14:00-17:30

    Hands on - Amina Echchiki (University of Lausanne and SIB) and Walid Gharib (University of Bern and 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.
    Friday 09 November 2018
    Hands on 09:00 - 12:30

    Hands on - Amina Echchiki (University of Lausanne and SIB) and Walid Gharib (University of Bern and 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.