Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage.

ABSTRACT: High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in

SUBMITTER: Valenzuela SL 

PROVIDER: S-EPMC9634423 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature