DL-GapFilling: a novel deep learning framework for improved plant genome gap filling

Genome assembly has been a cornerstone of bioinformatics for decades, with faster and more accurate assembly of unknown genomes remaining a critical challenge. However, genome diversity, structural variations, insufficient sequencing depth, and limitations of current algorithms often lead to numerous gaps during assembly, hindering the construction of high-quality reference genomes. While various assembly methods and software tools have been developed, most exhibit low efficiency in gap filling and fail to account for the intrinsic structural properties of genomic sequences. Here, we present DL-GapFilling, a deep learning-based framework for genome assembly and gap filling. DL-GapFilling leverages a novel Deep Filling Neural Network model to efficiently extract and contextualize flanking sequence information, and incorporates the BeamStar contraction-expand algorithm, which integrates a redefined cost function, an enhanced search strategy, and genomic structural priors to improve both generalization and efficiency in gap filling. In addition, a PredictionFilter mechanism is introduced to selectively retain high-confidence predictions, mitigating the impact of poorly predicted sequences on assembly quality. Experimental results demonstrate that DL-GapFilling significantly improves gap-filling performance across multiple plant or algal genome datasets, achieving increases of 15.6%, 6.1%, 16.7%, 5.5%, and 23.5% in the number of gaps filled compared to traditional tools, and outperforming existing DL-based methods in both efficiency and accuracy. These findings underscore the potential of DL-GapFilling as a powerful tool for advancing genome assembly research.