RegCloser: a robust regression approach to closing genome gaps

• Published in: BMC bioinformatics Vol. 24; no. 1; p. 249
• Main Authors: Cao, Shenghao, Li, Mengtian, Li, Lei M
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13.06.2023; BioMed Central; BMC
• Subjects: Applications software; Assembly; Closing gaps; Consensus; Copy number; Genetic research; Genome assembly; Genomes; Genomics; Graph theory; Layouts; Linear equations; Linear Models; Methods; Optimization; Parameter estimation; Parameter robustness; Regression analysis; Regression models; Robust regression; Robustness (mathematics); Software; Tandem repeat; Tandem Repeat Sequences; China; Genome assembly; Robust regression; Closing gaps; Tandem repeat
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05367-0

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. 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 estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads. RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser . The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.