Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.

ABSTRACT: Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkag

SUBMITTER: Do VH 

PROVIDER: S-EPMC10853769 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature