Viroscope

Viroscope provides biologically-informed genome assembly coverage analysis of high-throughput sequencing (HTS) data to improve precision and certainty in plant viral diagnosis.

Key Features:

• Biologically-Informed Genome Assembly Coverage: Leverages identification of viral replicases to establish genome coverage thresholds that reflect essential viral replication functions.
• Robust Diagnostic Pipeline: Delivers sensitive and specific viral detection across HTS datasets, including field samples, synthetic data, and published sequences, by focusing on replicase identification and genome coverage metrics.
• Standardization and Harmonization: Proposes standardized metrics and harmonized detection thresholds for HTS-based viral diagnostics to enable consistent interpretation across datasets.

Scientific Applications:

• Agricultural disease management: Supports accurate identification of plant viruses in agricultural and environmental contexts to inform disease management and control.
• Phytosanitary surveillance: Enables monitoring and mitigation of plant pathogen spread for phytosanitary agencies responsible for biosecurity and trade-related inspections.

Methodology:

Identifies viral replicases from HTS datasets and uses their presence to set biologically-informed genome assembly coverage thresholds for sensitive and specific viral detection across field samples, synthetic data, and published sequences.