Efficient iterative Hi-C scaffolder based on N-best neighbors.

ABSTRACT:

Background

Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task. However, the existing Hi-C based scaffolding tools either require a priori chromosome number as input, or lack the ability to build highly continuous scaffolds.

Results

We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors of contigs. Subsequent to scaffoldin

SUBMITTER: Guan D 

PROVIDER: S-EPMC8627104 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature