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R RAD seq exercise


Restriction site-associated DNA sequencing (RADseq) is recognized as one of the most important implementations in ecological genomics enabling low-cost massive genotyping also in non-model species. Although it has been implemented in many different ways, the basic idea is the non-random fragmentation of the whole genome by digestion with restriction enzymes and sequencing of restriction sites flanking DNA fragments on a high-throughput sequencing platform. Several software packages (e.g., Stacks) have been developed for analyzing RADseq data. Here you will learn how to manipulate and analyze RADseq data, from filtering of the raw sequencing reads to simple population genomic analyses, in the R environment using standard R functions and functions from the Bioconductor packages.

If you are not familiar with RADseq library preparation, here is a brief overview.
Further information about RADseq is summarized nicely in this recent review.