Abstract
Motivation Long read technologies have made a revolution in de novo genome assembly by generating contigs of size orders of magnitude more than that of short read assemblies. Although the assembly contiguity has increased, it still does not span a chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scalable and computationally efficient scaffolding method that can boost the contiguity of the assembly by a large extent using genome wide chromatin interaction data such as Hi-C. Particularly, we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies.
Results We tested our methods on two long read assemblies of different organisms. We compared our method with previously developed method and show that our approach performs better in terms of accuracy of scaffolding.
Availability The software is available for free use and can be downloaded from here: https://github.com/machinegun/hi-c-scaffold
Contact jchin{at}pacificbiosciences.com
