ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

Background With the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data is becoming increasingly available. This data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been experimentally shown to be a driving force for many genomic functions from regulation to transcription. Thus, the Three Dimensional Genome Reconstruction Problem seeks to take Hi-C data and produce the complete physical genome structure as it appears in the nucleus for genomic analysis. Results We propose and develop a novel method to solve the Chromosome and Genome Reconstruction problem based on the Bat Algorithm which we called ChromeBat. We demonstrate on real Hi-C data that ChromeBat is capable of state of the art performance. Additionally, the domain of Genome Reconstruction has been criticized for lacking algorithmic diversity, and the bio-inspired nature of ChromeBat contributes algorithmic diversity to the problem domain. Conclusions ChromeBat is an effective approach at solving the Genome Reconstruction Problem. The source code and usage guide can be found here: https://github.com/OluwadareLab/ChromeBat .