Mapping to a Reference Genome Structure

TL;DR

This paper proposes a framework for representing reference genomes with mapping schemes, including graph-based models to account for genetic variation, enhancing comparative and medical genomics research.

Contribution

It introduces the concept of reference structures, detailing their properties and illustrating how graph-based models can better represent genetic diversity.

Findings

Defined desirable properties of reference structures

Presented examples of reference structures including graphs

Showed how graphs can model genetic variation effectively

Abstract

To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a collection of one or more reference genomes and a scheme for mapping to their positions as a reference structure. Here we describe the desirable properties of reference structures and give examples. To account for natural genetic variation, we consider the more general case in which a reference genome is represented by a graph rather than a set of phased chromosomes; the latter is treated as a special case.