SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.

ABSTRACT: Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequ

SUBMITTER: Liu X 

PROVIDER: S-EPMC12286774 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature