rearrvisr: an R package to detect, classify, and visualize genome rearrangements

Abstract

The identification of genome rearrangements is of direct relevance for understanding their potential impacts on evolution and disease. However, available methods that detect or visualize rearrangements from deviations in gene order do not map them onto a genome of interest, complicating downstream analysis. In this work, we present rearrvisr, an R package that implements a novel algorithm for the identification and classification of rearrangements. In contrast to other software, it projects rearrangements onto a single genome, facilitating the localization of rearranged regions and estimation of their extent. We show that our tool achieves high precision and recall scores on simulated data, and illustrate the utility of our method by applying it to a data set generated from publicly available Drosophila genomes. The package is freely available from GitHub (https://github.com/dorolin/rearrvisr) and can be installed directly from R.