Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs

For a long time, the construction of complete reference genomes for complex eukaryotic genomes has been hindered by the limitations of sequencing technologies. Recently, the Pacific Biosciences (PacBio) HiFi data and Oxford Nanopore Technologies (ONT) Ultra-Long data, leveraging their respective advantages in accuracy and length, have provided an opportunity for generating complete chromosome sequences. Nevertheless, for the majority of genomes, the chromosome-level assemblies generated using existing methods still miss a high proportion of sequences due to losing small contigs in the step of assembly and scaffolding. To address this shortcoming, in this paper, we propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs. Experimental results on both real and simulated datasets demonstrate that this method is able to improve the completeness of the chromosome-level assembly.