ViraLM: empowering virus discovery through the genome foundation model.

ABSTRACT:

Motivation

Viruses, with their ubiquitous presence and high diversity, play pivotal roles in ecological systems and public health. Accurate identification of viruses in various ecosystems is essential for comprehending their variety and assessing their ecological influence. Metagenomic sequencing has become a major strategy to survey the viruses in various ecosystems. However, accurate and comprehensive virus detection in metagenomic data remains difficult. Limited reference sequences prevent alignment-based methods from identifying novel viruses. Machine learning-based tools are more promising in novel virus detection but often miss short viral contigs, which are abundant in typical metagenomic data. The inconsistency in virus search results produced by available tools further hig

SUBMITTER: Peng C 

PROVIDER: S-EPMC11631183 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature