RADstackshelpR: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) (<doi:10.1111/mec.15253>) 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)
(<doi:10.1111/2041-210X.12775>) which establishes clear
recommendations for optimizing the parameters 'm', 'M', and
'n', during the process of assembling loci.
