RegCloser: a robust regression approach to closing genome gaps.

ABSTRACT:

Background

Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter.

Results

We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter

SUBMITTER: Cao S 

PROVIDER: S-EPMC10265787 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature