Next generation SNP data: experimental design and analysis - a joint course with CUSO

26 - 29 March 2012

A joint course with CUSO Doctoral Program StarOmics.

Organizers: Philippa Griffin and Yvonne Willi (University of Neuchâtel).



  • To highlight the scope for creative, large-scale experiments to bridge the gap between molecular and ecological evolution using new sequencing technologies.
  • To introduce methods for obtaining large-scale SNP datasets to tackle evolutionary and ecological questions.
  • To teach initial data processing and some further, question-specific analysis of such SNP datasets.

Content and pre-course assignment

The use of next-generation sequencing methods (including RAD-Tag sequencing) to produce large SNP datasets is revolutionizing evolutionary ecology. These methods can be applied to population genetics, genomic mapping and phylogenetic studies of model and non-model organisms.

This course will cover the following:

  • Introduction to RAD-Tag sequencing and related methods
  • Experimental design: how to design SNP experiments to suit your research questions, your organism of interest, and your budget
  • Initial data processing (using R, Galaxy and Stacks): quality control and data filtering steps, sequence alignment, SNP detection and validation
  • Downstream analysis: scaling up traditional population genetic structure, genomic selection and phylogenetic analyses for large SNP datasets.

Preliminary Reading :

1. Rowe HC, Renaut S, Guggisberg A. RAD in the realm of next-generation sequencing technologies. Mol Ecol 2011 Sep.;20(17):3499–3502.

2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE 2008 Oct.;3(10):e3376.

3. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 2011;6(5):e19379.

4. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags. PLoS Genet 2010 Feb.;6(2):e1000862.

5. Catchen J, Amores A, Hohenlohe P. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes 2011;1:171–182.

6. Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Sciences 2010 Sep.;107(37):16196–16200.

Sponsoring :

Access to the Amazon Cloud and JoinMap thanks to donations from Scott Handley (http://evomics.org/) and Johan W. Van Ooijen (the JoinMap author).

General information

Dates:  26 - 29 March 2012

Schedule 8.55 - 17.00

Location University of Neuchâtel, Faculté des sciences, UniMail, building C  (C001 Animalerie)

Credit points 2.0 credit points  (Research tools, DP) 

Evaluation Full attendance and active participation

Information Please contact the scientific organizers Philippa Griffin or Yvonne Willi, or the doctoral program coordinator Christiane Bobillier (administration)

Travel expenses :  participants in the Interuniversity Doctoral Program in Organismal Biology are eligible for reimbursement of incurred travel expenses by train (half-fare card, and 2nd class)

  • Send the original tickets (no copies) with the reimbursement form  to Dr. Christiane Bobillier. No reimbursement for GA, bus, taxi or car travel expenses will be paid.
  • For "CUSO doctoral program StarOmics participants: see information on the web site.

(no attestation will be sent by mail)


  • This workshop is opened to all Ph.D. students, however priority is given to PhD students participating in the doctoral program in organismal biology and CUSO StarOmics doctoral program until 30 January 2012.
  • Post-docs and master students are welcome as long as places are available.
  • Maximum number of participants: 25
  • As numbers are limited, applicants are requested to submit a short letter (max. 300 words) describing their past experience in this field, their current research and its relevance to this workshop. This letter should be sent to Dr Philippa Griffin .
    Participants will be informed on 20 February if they can participate or not.

Registration through the web only: closed

Please note the cancellation policy (CHF 200) .

Deadline: 15 February 2012