maize-genetics/rPHG: R front-end for the practical haplotype graph

The aim of rPHG is to develop an R API for the practical haplotype graph (PHG). The PHG is a trellis graph based representation of genic and intergenic regions (called reference ranges or reference intervals) which represent diversity across and between taxa. It can be used to: create custom genomes for alignment, call rare alleles, impute genotypes, and efficiently store genomic data from many lines (i.e. reference, assemblies, and other lines). Skim sequences generated for a given taxon are aligned to consensus sequences in the PHG to identify the haplotype node at a given anchor. All the anchors for a given taxon are processed through a Hidden Markov Model (HMM) to identify the most likely path through the graph. Path information is used to identify the variants (SNPs). Low cost sequencing technologies, coupled with the PHG, facilitate the genotyping of large number of samples to increase the size of training populations for genomic selection models. This can in turn increase predictive accuracy and selection intensity in a breeding program.

install.packages("remotes")
remotes::install_github("maize-genetics/rPHG")