Integrative Assessment of Pathogenic Bacterial Genomes: Insights from Quality Metrics

Abstract

Genomic resources are increasingly being shared in public databases for reusability. Ensuring the quality of these resources is crucial, as the presence of low-quality genomes can compromise downstream analyses and propagate across databases. However, there is a lack of consistent and comprehensive assessments for such genomes in public genomic databases. This study focused on the quality assessment of 474 pathogenic bacterial genomes submitted from South Korea, with a particular emphasis on the integrative application of completeness, contiguity, and accuracy metrics. The genomes were ranked based on cumulative scores derived from individual metrics. High-ranked genomes consistently exceeded defined thresholds, including 98% completeness for complete single-copy BUSCO, less than 200 contigs, N50 values greater than 65 kb, and unmapped reads below 2%. Notably, positive and negative linear associations were observed among these quality metrics, emphasizing their integrative utilization, although the consistency across all metrics varied. The findings emphasize the importance of conducting comprehensive genome assessments and implementing stringent quality control measures in public databases to enhance the reliability and usefulness of pathogenic bacterial genomic data. By addressing these issues, we can improve the overall quality of public genomic resources and ensure their suitability for diverse downstream applications.