Winter School B@G 2015
Bioinformatics for Adaptation Genomics: Adaptation genomics in the realm of Next-Generation Sequencing data analysis
Venue: Alexander & Gerbi Hotel, Weggis, Switzerland
Date: March 1st – 7th 2015
The rapid development of next-generation sequencing technologies and their application to adaptation genomics research holds great promise to increase our understanding of genotype-phenotype-environment interactions, and the pioneering findings of recent years have inspired the launching of genome-scale projects in an ever-increasing number of organisms. A great effort has been made to develop software that can handle the large datasets that typically characterise ecological genomics studies, while still providing robust analytical platforms for supporting their application in non-model systems. However, due to the sheer number and complexity of available packages, it is often difficult for investigators to assess the potential and limitations of alternative methods, and determine which are best suited for their particular question and dataset. This winter school aims at providing an opportunity for investigators to gain insight into the rationale behind some of the established analytical pipelines in adaptation genomics research and acquire knowledge on the best practice to perform analyses and experimental design.
The School aims to address primarily evolutionary biologists and bioinformaticians who want to gain deeper knowledge on state-of-the-art methods to detect adaptive patterns from genome-wide nucleotide data. Applications from early career researchers (PhD and post-doctoral level) as well as faculty with a background in ecology, genetics, or bioinformatics will be considered. The workshop is particularly aimed at candidates with experience of the Unix environment and with previous practice on analytical pipelines for genomic data. Participants will be requested to bring their own laptop with which to connect to the server for the practical sessions.
The workshop will be limited to 20 participants.
Aim & Objectives
The Winter School provides an opportunity for investigators to penetrate the ‘black box’ behind the complex approaches available for investigating adaptation genomics throughout the analytical pipeline; from the assumptions and requirements necessary to produce a high quality SNP dataset from raw next-generation sequence data, to the in-depth interpretation of methods designed to detect signature of selection, demographic patterns and associations between genotypes and environment, and/or phenotypes.
Specifically, the following objectives will be addressed:
- the rationale and assumptions intrinsic to different available analytical approaches
- comparison of the implementation and results of alternative analytical methods as applied on the same or similar datasets
- interpretation of the outputs from these programs at different stages in the analysis.
- best practice to implement the available packages when addressing different evolutionary questions, and how this conditions experimental design
Lessons will include initial lectures on the theoretical background of the programs and practical demonstrations given by the instructor followed by hands-on exercises performed by the participants under guided supervision. Computing activity will rely on individual connections to the Genetic Diversity Centre (GDC, ETH Zurich) server that will provide resources for demonstrations and practical training. Emphasis will be given to interpretation of the output of the programs with slots of discussion time allowed to facilitate interactions between the instructor and the audience.