Evaluating Reference-Independent Pipelines for the Detection of Spreading Organisms in Metagenomic Datasets (opens in new tab)

The emergence of unidentified pathogens, or "Disease X," poses a significant threat to global health, necessitating the development of proactive surveillance strategies for the wildlife and human virosphere. Since novel viruses often lack universal genetic markers or known homologs, this study evaluates four reference-independent computational pipelines: coverage-based, k-mer-based, nucleotide clustering, and Large Language Model (LLM)-based designed to detect spreading organisms by comparing...