alberto-rodriguezizquierdo/airen_r: A R package to optimize the performance of Restriction digestion to improve the resolution of GBS

Genotyping By Sequence (GBS) approaches combine the use of restriction enzymes, sample indexing,and NGS to allow the genotyping and epigenotyping of large populations, helping to the identification of genes regulating, for example, adaptation to environmental stress. Selection of restriction enzymes is a key step to optimize the quality of GBS. Tools like SimRAD in R environment partially help to solve this problem, giving a prediction of the number of fragments and their size generated by a give enzyme. However, such results are not accurate enough because of the low profundity of the analysis. Consequently, the aim of this project is to develop a bioinformatic tool that allows for a informed choice of the best restriction enzymes to be used during the GBS analysis of grapevine genotype or set of genotypes to obtain the best sequencing resolution. Because of this resolution, this tool allows to choose the best enzymes depending on the nature of the study (for example, to cut inside or near the gene in genotyping or detecting epigenomic events, respectively).

install.packages("remotes")
remotes::install_github("alberto-rodriguezizquierdo/airen_r")