Optimize the De Novo Stacks Pipeline via R
Offers a handful of useful wrapper functions which streamline
the reading, analyzing, and visualizing of variant call format (vcf) files in R.
This package was designed to facilitate an explicit pipeline for optimizing
Stacks (Rochette et al., 2019) (<10.1111>)
parameters during de novo (without a reference genome) assembly and variant
calling of restriction-enzyme associated DNA sequence (RADseq) data. The
pipeline implemented here is based on the 2017 paper "Lost in Parameter Space"
(Paris et al., 2017) (<10.1111>) which
establishes clear recommendations for optimizing the parameters
'm', 'M', and 'n', during the process of assembling loci.10.1111>10.1111>