Scaffolding of long read assemblies using long range contact information

Background Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually does not reconstruct a full chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To increase the contiguity of the assembly to the chromosome level, different strategies are used which exploit long range contact information between chromosomes in the genome. Methods We develop a scalable and computationally efficient scaffolding method that can boost the assembly contiguity to a large extent using genome-wide chromatin interaction data such as Hi-C. Results we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies. We tested our methods on the human and goat genome assemblies. We compare our scaffolds with the scaffolds generated by LACHESIS based on various metrics. Conclusion Our new algorithm SALSA produces more accurate scaffolds compared to the existing state of the art method LACHESIS. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3879-z) contains supplementary material, which is available to authorized users.