Lost in parameter space: a road map for stacks

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Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics (2019, methodology): “Our experience is that with the development of proper analyti‐ cal protocols (Paris, Stevens, & Catchen, 2017; Rochette & Catchen, 2017), and with supportive software, we can close the performance gap between RAD studies and secure a successful experimental strategy for the next decade.”
Deriving genotypes from RAD-seq short-read data using Stacks (2017, background): “44, which involves running series of de novo analyses with different parameter values and monitoring the number of polymorphic RAD loci found in 80% of samples or more (the r80 loci), until a stable set of values for M, n, and m is found.”