Galaxy Community Conference 2016 (GCC16)

→ Slides, doi: 10.7490/f1000research.1112912.1
→ Video

RADseq1 data allow scientists to gather genome wide information with a low-cost approach compared to complete genome sequencing. In this training session, we will show how to analyze RADseq data to

1. build genetic maps2,
2. calculate population genomics statistics3,4 and
3. assemble paired-end loci with or without reference genome using Stacks5 on Galaxy

Stacks works with restriction-enzyme based data, including GBS, CRoPS, and single and double digest RAD. Stacksidentifies loci in a set of individuals, either de novo or aligned to a reference genome (including gapped alignments), and then genotypes each locus. See the Stacks Manual for full details. 

Stacks has been integrated into Galaxy and is available via the GUGGO Tool Shed.

Prerequisites:

• A general knowledge of Galaxy (for example, you should be familiar with the material in Galaxy 101 or have attended Introduction to Galaxy).
• A wi-fi enabled laptop with a modern web browser.  Google Chrome, Firefox and Safari will work best. 

1. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research. 17(2):240-248.

2. Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH. (2011) Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication. Genetics 188(4):799-808.

3. Davey JW and Blaxter ML (2011) RADSeq: next-generation population genetics. Briefings in Functional Genomics. 10 (2): 108

4. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. (2012) Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE 7(5): e37135.

5. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. (2011) Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3 1(3):171-182