Lost in parameter space: a road map for stacks

Summary Restriction site‐Associated DNA sequencing ( RAD ‐seq) has become a widely adopted method for genotyping populations of model and non‐model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks . Using three empirical RAD ‐seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks . By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core…

• UO
  University of Exeter