e-learning
RAD-Seq de-novo data analysis
Abstract
In the study of Hohenlohe et al. 2010, a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback Gasterosteus aculeatus was conducted. Authors used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How to analyze RAD sequencing data without a reference genome for a population genomics study?
Learning Objectives
- Analysis of RAD sequencing data without a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics from RAD sequencing data
Licence: Creative Commons Attribution 4.0 International
Keywords: EBV dataset, EBV workflow, Ecology, RAD-seq, biodiversity, genetic composition EBV class, species populations EBV class
Competency level: • Beginner
Target audience: Students
Resource type: e-learning
Version: 15
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
Learning objectives:
- Analysis of RAD sequencing data without a reference genome
- SNP calling from RAD sequencing data
- Calculate population genomics statistics from RAD sequencing data
Date modified: 2026-05-07
Date published: 2017-02-14
Authors: 
Yvan Le Bras
Contributors: Gildas Le Corguillé, Niall Beard, Verena Moosmann, William Durand, Björn Grüning, Bérénice Batut, Helena Rasche, Nicola Soranzo, Saskia Hiltemann, Wolfgang Maier, Yvan Le Bras, Marie Josse
Scientific topics: Ecology, Biodiversity
Activity log
