The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.

ABSTRACT:

Motivation

Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

Results

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service. The PHG has already been able to accurately

SUBMITTER: Bradbury PJ 

PROVIDER: S-EPMC9344836 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature