Workshop Description

Restriction site Associated DNA Sequencing (RAD-Seq) sequences short regions immediately flanking restriction sites. RAD-Seq enables cost-effective marker discovery and genotyping of hundreds of thousands of genetic markers in hundreds of samples in ANY species, with or without a reference genome. This three-day workshop will practice hands-on analysis of RAD-Seq data. We will use popular stacks pipeline ( to de novo assemble RAD loci for species lacking a reference genome.

Day 1

  • RADseq Basics
  • RADseq data characteristics
  • Algorithmic details of stacks pipeline

Slides for day 1 can be found here.

Day 2

  • Run the stacks pipeline from raw reads to de novo assemble RAD tag loci.
  • Apply various filters, call variants and estimate summary statistics of genetic variation.

Slides for day 2 can be found here.

Day 3

  • PCA analysis to detect population structure

Slides for day 3 can be found here.

Technical Requirements


Ying Zhen is a postdoc working with Kirk Lohmueller and Tom Smith. Her research focuses on using NGS data to study the demographic history and natural selection of non-model species from Central Africa. Ying was a postdoc with Peter Andolfatto at Princeton University, working on convergent evolution in insects and gene expression evolution in Drosophila. She received her Ph.D. from Kansas State University where she worked on evolution of freezing tolerance.


Workshop Details

Prerequisites: W1, 2, & 3
or equivalent knowledge
Length: 3 days, 2-3hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall 2018 Dates

Sorry! Will return in Winter 2019.