EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends.

ABSTRACT:

Background

The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding tools, which count Hi-C links between contigs using the whole or a large part of contig regions. As the Hi-C links of two adjacent contigs concentrate only at the neighbor ends of the contigs, larger contig size will reduce the power to differentiate adjacent (signal) and non-adjacent (noise) contig linkages, leading to a higher rate of mis-assembly.

Results

We design and develop a novel Hi-C based scaffolding tool EndHiC, which is suitable to assemble large contigs into chromosomal-level scaffolds. The core idea behind EndHiC, which distinguishes it f

SUBMITTER: Wang S 

PROVIDER: S-EPMC9730666 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature