Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.

ABSTRACT:

Background

Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be "searching followed by evaluation", which is infeasible for long gaps, or "searching by evaluation", which heavily relies on heuristics and thus usually yields unreliable contig paths.

Results

We here report an accurate and efficient approach to filling gaps of genome s

SUBMITTER: Huang B 

PROVIDER: S-EPMC8557617 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature