ForBio course: RADseq/Stacks

The objective of this course is to familiarize with the use of next generation sequence data produced from Reduced Representation Libraries (RRL) approaches such as Restriction site Associated DNA (RAD-tags). These libraries are often used for genotyping by sequencing, and can provide a dense set of single nucleotide polymorphism (SNP) markers that are spread evenly across a genome. These markers are useful for a variety of genetic and genomic analyses in model and non-model organisms. Students will gain experience with the computational pipeline Stacks that was designed for the analysis of such data. Data will be analyzed de novo to perform a population analysis without the aid of a reference genome, and from an organism with a reference genome to identify signatures of selection. Stacks can be used for other analyses of RAD-seq data as well, such as constructing genetic maps and phylogeography, although those are beyond the scope of this exercise.

Students will learn how to:
1. Prepare raw RAD Illumina data for analysis by removing low quality reads and de- multiplexing a set of barcoded samples.
2. Use Stacks to assemble RAD-tags de novo from several populations of samples.
3. Call SNPs, genotypes, and haplotypes of these individuals within Stacks.
4. Export data from Stacks for analysis in Structure.
5. Align RAD sequences against a reference genome.
6. Use Stacks to perform genome scans using population genetics statistics like FST.
7. Use Stacks to generate RAD loci in order to build phylogenetic trees.
By the end of this workshop you will be expected to know how to:
8. Manipulate raw RAD Illumina data for analysis using a variety of different parameters.
9. Produce de novo assemblies using reads from an organism without a reference genome.
10. Align RAD tags against a reference genome to identify signatures of selection.
11. Extend what was learned to more complicated ‘on your own’ problems.

Course teachers: Julian Catchen and Nicolas Rochette.

The course will be taught at the Finse Alpine Research Center on the breathtakingly scenic Handangervidda. Finse can be reached by train from Oslo and Bergen.

There is no registration fee for the course, and food and accommodation is included for all ForBio members. ForBio members that are graduate students or postdocs in Norway can have travel expenses covered. All ForBio members have accommodation and food expenses covered. ForBio associates will need to pay 3500 NOK for food and accommodation.A schedule is available here. Register here. Extended application deadline is May 15th, 2017.

A 2 ECTS course certificate will be given to students that pass the course by ForBio.

Contact Hugo de Boer ( for more information.

Published Feb. 20, 2017 10:09 AM - Last modified May 1, 2017 3:07 PM