SVPopEx: Population-Wide Visualization and Exploration of Structural Variants

Abstract

Structural variants (SVs) are large-scale genomic variants, which can disrupt important functional and regulatory elements, leading to genomic disorders in humans and playing important roles in domestication, disease resistance, and traits in plants. SVs are generated across populations of individuals and used for association studies, consisting of large datasets with thousands of genomic loci. Visualization of these SVs aids in understanding their genomic distribution, identifying patterns across affected or phenotypic groups, and assessing their proximity to other genomic regions of interest. A variety of tools exist for visualizing SVs, including linear genome browsers and graph-based methods; however, many do not offer intuitive or scalable representations of SVs across large populations. To address this, we present SVPopEx, an interactive tool for population-wide visualization and exploration of SVs. SVPopEx provides a unique and intuitive representation for insertions, deletions, inversions, duplications, and translocations in a linear genome-style browser. Novel features were developed to support comparisons across genomes within user-defined regions, including rendering SVs based on one or more samples and visualizing haplotypes. Use of the tool is demonstrated with SV datasets from Schistosoma mansoni and Lens culinaris. A task-based evaluation was conducted using SVPopEx and two other linear genome browsers, which demonstrated that SVPopEx excelled in (1) providing a clear representation of the SVs present and (2) supporting comparisons across genomes.