Viroscope comprises an entire RNA high-throughput (HTS) data analysis pipeline that performs read assignment, de novo assembly with reference-based mapping, and pseudo-annotation to generate VGAC metrics (Viral Genome Assembly Coverage) and viral replica identification.
The Viroscope pipeline comprises two independent phases for plant virus diagnostics based on HTS data. First, a thorough data processing stage that includes: (1) read assignment, (2) de novo assembly of assigned reads, (3) reference mapping of assembled contigs, (4) genome coverage calculation of mapped contigs, (5) consensus calling, and (6) replicase detection in consensus sequences. In the second step, Viroscope detects pathogens by considering the VGAC values obtained by three read assignment algorithms and the identification of replicases. The validation of the pipeline was performed with three types of datasets: field samples from a farm, simulated datasets, and publicly available datasets (including different library preparation methods and sequencing technologies). To evaluate and research diagnostic sensitivity following the various cutoff values explored, the Viroscope results for field samples were further confirmed using RT-PCR techniques.

Dr. Md. Monirul Islam
Senior Scientist

Fig: Overview of the Viroscope, the data analysis pipeline, and the experimental validation strategy