Scaffolding of long read assemblies using long range contact information.

ABSTRACT:

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 longe

SUBMITTER: Ghurye J 

PROVIDER: S-EPMC5508778 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature