Analysis of whole-genome sequence data: assessment of polymorphisms of individual and pooled samples, and genome-wide association study

17 - 20 February 2014

A joint course with CUSO doctoral program StarOmics

Organizers: Prof. Dr Yvonne Willi, University of Neuchâtel & Dr Christiane Bobillier, University of Neuchâtel



Dr Robert Kofler , Verterinärmedizinische Universität Wien, Austria

Prof. Dr Zoltan Kutalik , University of Lausanne, Switzerland

Dr Alexander Platzer , Gregor-Mendel Institut of molecular plant biology, Wien, Austria


To get familiar with a variety of analyses on whole-genome sequence data

Requirements and pre-course assignment

Requirements: Basic knowledge of UNIX commands

This may help you to revise for the course:

Unix command summary with tutorial

http://www.cheatography.com/davechild/cheat-sheets/linux-command-line/ (very compressed)

https://help.ubuntu.com/community/CommandlineHowto/ (very basic starting point)

http://freeengineer.org/learnUNIXin10minutes.html (quite much for the 10 minutes. The vi editor there is not a must)

http://linuxcommand.org/lc3_learning_the_shell.php (with more text and only half the same as the one before)

http://askubuntu.com/questions/20034/differences-between-doublequotes-singlequotes-and-backticks-on-comm (one particular topic which makes often troubles)

Pre-course assignments: Reading of the following papers. More information will be sent to registered participants.

Robert Kofler:

A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster Héloïse Bastide, Andrea Betancourt, Viola Nolte, Raymond Tobler, Petra Stöbe, Christian Schlötterer, Andreas Futschik

Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America Daniel K. Fabian, Martin Kapun, Viola Nolte, Robert Kofler, Paul S. Schmidt, Christian Schlötterer, Thomas Flatt

Alexander Platzer:

A quite concise overview for the aligners for NGS data

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
(In the way it is written it is not easy to get everything, but the figures are summarizing a lot of the general topic)


Topic 1 : Mapping reads to reference genome, SNP & indel discovery

Reminder of important UNIX commands
Data file formats and software
Mapping reads to reference genome
SNP discovery
Indel discovery

Topic 2 : Pooled whole-genome re-sequencing, SNP-frequency data and down-stream analysis

Pool-seq with a single population (PoPoolation1)
Pool-seq with several populations (PoPoolation2)
Gene set enrichment analysis from the results of 1 and 2 (Gowinda)

Topic 3 : GWAS – genome-wide association studies: hunt for variants underlying common diseases 

GWAS basics:

Necessary data sets
How to test associations
How to declare significance?
Some typical studies
Population stratification

GWAS advanced Topics:

Gene-environment interaction
Pathway analysis
Total explained heritability
Uncertain genotype association

Exercises on computers are organized.

General information

Date:   Monday 17 to Thursday 20 February 2014

Schedule: 8.55 -17.30

Location: University of Neuchâtel, Faculté des sciences, UniMail, building C room 001 and Millenium computer room E026

Credit point: 2.0 credit point (Research tools)

Evaluation: Full attendance, active participation including preparation (home work as described)

Information: Please contact  the doctoral program coordinator Dr. Christiane Bobillier

Registration fee : Free for Ph.D. students of DP-biol in Organismal Biology participants and CUSO StarOmics. CHF 30.00 for all other participants. It includes lunch on the first day and mornings coffee breaks.

Lunch and coffee breaks : Lunch on the first day is included as well as the morning coffee breaks. Afternoon coffee breaks and lunches on days 2 to 4 can be taken at the Cafétéria of UniMail (menu CHF 10, salad bar).

Travel expenses:

For participants of the CUSO doctoral program StarOmics, see CUSO StarOmics web site .

For participants of the DP-biol doctoral program in Organismal biology, click here

You are not a member of DP-biol? Why not register now? It's free!


This course is open to all, with priority to PhD students of the doctoral programs CUSO StarOmics and DP-biol in Organismal biology (free), external (CHF 30.00).

Maximum number of participants: 22

To apply, send (email) a short letter of motivation (max 1 page) (with the signature of your supervisor if you are a PhD student) to Dr Christiane Bobillier.

Deadline: 28 January 2014 Registration CLOSED

Please note the cancellation policy (CHF 30).