Program

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Sunday February 28th

Arrival and welcome

10:00 - 18:00 Arrival and registration of participants – Alexander & Gerbi Hotel   

19:00 Welcome and introductory talk

20:00 Opening dinner

EXTRACTING SNP DATA FROM NGS READS

Monday February 29th

Part 1: Rad SNPs from RADseq - The bioinformatics of reduced representation libraries

Dr. Jonathan Puritz (Harte Research Institute, Texas A&M Corpus Christi, USA)

Session 1 - An overview of the many different RAD techniques, RAD experimental design, and minimizing bias in the laboratory

Session 2 - Pipelines, software packages, and scripting - how to generate SNPs from RADseq data

Session 3 - Skimming SNPs from the top: techniques for filtering RADseq SNPs


Tuesday March 1st

Part 2: Whole Genome and Exome Datasets

Mr. Erik Garrison (Wellcome Trust Sanger Institute, UK)

Session 1 - Overview and theory of SNP and indel calling from NGS data; approaches, pitfalls and best practice

Session 2 - Case studies in variant calling: germlines, populations, somatic variation, pools, polyploids, haplotypes, and structural variants

Session 3 - Hands-on real data

INFERENCE OF EVOLUTIONARY SIGNAL FROM SNP DATA

Wednesday March 2nd

Part 1: Detection of signatures of selection  

Dr. Matteo Fumagalli (University College London, UK)

Session 1 - The effect of selection on the genome + Methods to detect selection signals (positive, negative, balancing)

Session 2 - The problem of assessing significance + Critical discussion of case studies

Session 3 - Practical: genomic scan for selection from large-scale data set

 

Thursday March 3rd

Part 2: Inferring complex demographies from genomic data

Prof. Dr. Daniel Wegmann (University of Fribourg, Switzerland)

Session 1 - Estimating diversity from NGS data: the problem of filtering and some solutions.

Session 2 - Inferring complex demographies from frequency spectra using composite likelihood approaches.

Session 3 - Inferring complex demographies using Approximate Bayesian Computation

 

Friday March 4th

Part 3: GWAS

Prof. Dr. Arthur Korte (Center for Computational and Theoretical Biology, University Würzburg, Germany)

Session 1 – Introduction into genome-wide association mapping

Session 2 – Complex GWAS models / state of the art analysis

Session 3 – Real data analysis with custom R scripts and web tools

 

20:00 Closing dinner (Swiss speciality)

 

Saturday March 5th

Breakfast and Departure

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