DEGAP: Dynamic Elongation of a Genome Assembly Path

Genome assembly remains to be a major task in genomic research. Despite the development over the past decades of different assembler software programs and algorithms, it is still a great challenge to assemble a complete genome with no gaps. With the latest DNA Circular Consensus Sequencing (CCS) technology, several assembler programs now can build a genome from raw sequencing data to contigs, however, some complex sequence regions remain as unresolved gaps. Here, we present a novel gap-filling software DEGAP that can resolve gap regions in genomes by utilizing the dual advantages of accuracy and length of high-fidelity (HiFi) reads. DEGAP optimizes HiFi reads by identifying the differences between reads and provides ‘GapFiller’ or ‘CtgLinker’ modes to eliminate or shorten gaps in genomes. DEGAP adopts a cyclic elongation strategy that automatically and dynamically adjusts parameters according to the complexity of the sequences and selects the optimal extension path. DEGAP has already been successfully applied to decipher complex genomic regions in several projects and may be widely employed to generate more gap-free genomes.