Welcome to RADCamp
Over the last 10 years biogeographers have increasingly transitioned from investigating phylogeographic patterns in space and time using datasets composed of one or only a handful of markers to massive datasets containing thousands or tens of thousands of “anonymous” nuclear loci generated using restriction site associated DNA sequencing (RAD-Seq). These larger datasets provide more robust phylogenetic estimates, and can provide additional sources of information such as evidence of historical introgression. The process of organizing and making sense of the vast quantities of reads that come back off a sequencing instrument is non-trivial, and of great consequence.
RADCamp workshops are designed to introduce ipyrad, a unified and self-contained RAD-Seq assembly and analysis framework, which emphasizes simplicity, performance, and reproducibility. In these workshops we proceed through all the steps necessary to assemble a typical RAD-Seq dataset. Additionally, we introduce the ipyrad ‘analysis’ API which provides a powerful, simple, and reproducible interface to several widely used methods for inferring phylogenetic relationships, population structure, and admixture.
What is RAD-Seq?
- A canonical introduction: Andrews et al 2016
- A thorough review of reduced representation protocols: Campbell et al 2018
Who should attend?
RADCamp workshops are normally geared toward practicing field biologists with little or no computational experience.
Workshop attendees will need to bring a laptop computer.
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2), 81.
Other cool RAD-seq workshops with useful online resources:
PoreCamp - Which inspired the design of this workshop and also of this site.