Whole genome sequencing work-shop

1-2 October 2015

Emanuel Schmid, Post-doctorant, Institut suisse de bioinformatique (ISB)/Vital-IT

(Gina M. Cannarozzi, Ph. D. Institute of Plant Sciences, University of Bern) replaced by Debora Gasperini, Post-doctorant, Department of Plant Molecular Biology, University of Lausanne

Laurent Falquet, Department of Biology Fribourg

Hannes Svardal, Post-doctorant, Gregor Mendel Institute, Austria

Practical Part:

Emanuel Schmid, Post-doctorant, Institut suisse de bioinformatique (ISB)/Vital-IT

Amel Bekkar, Doctoral researcher, Institut suisse de bioinformatique (ISB)/Vital-IT

Martial Sankar, Research Assistant, Institut suisse de bioinformatique (ISB)/Vital-IT

In the last few years the price for whole-genome sequencing dropped continuously and recently the 1000$ genome barrier was announced to be broken (under certain circumstances) see Nature news. This facilitates the de novo but as well the re-sequencing of many genomes, especially for large eukaryotic genomes. One new technique which evolved e.g. from these developments is the whole genome re-sequencing to identify mutants in mutagenesis screens.

In the herewith proposed work-shop two topics might be presented and complemented by a hands-on experience and talks of external speakers:

a.) de novo sequencing of genomes (brief). The goal is two show the participants a work-flow, how to evaluate the raw data (NGS reads), prepare them and use common assemblers to generate a first draft assembly. Topics to discuss will be the different nature of the raw-reads (Hiseq, mate-pair, paired-end or long reads), common expressions (such as contigs, unitigs, scaffolds, phred-score,..) and ways to compare genomes. A special focus will be drawn on how to measure the quality of an assembly and how to verify its completeness.

b.) re-sequencing of genomes (extensive) to cover the demands from many groups to present such a topic, a special focus will be drawn on how to identify mutations in model organism after mutagenesis. The model organism of choice might be Arabidopsis since the initial demand for such a work-shop derived from the plant community in Lausanne. Accompanied with a hands-on session, students will be shown how to treat the raw-data of NGS, assure quality and properly map them against the model genome. Analysis of SNPs and/or other mutation will be shown, together with ways how to determine the effect of mutations on the gene functionality. This session will be followed by an extensive hands-on workshop.

UNIL SORGE, Génopode, 1015 Lausanne

Day1- Talks

8.30 - 17.00 Session 1: Gina Cannarozzi

Biological background, EMS mutagenesis, designing screens,importance of ploidy,..

Session 2: Laurent Falquet

Genome sequencing and assembly

Session 3: Hannes Svardal

SNP detection and analysis


Day2 - Practicals

9.00 - 16.00: Practicals

Up-to-date program and information:
edu.isb-sib.ch

CUSO PhD students: Free

External participants: 100.- CHF

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