Discovery of Tobamoviral Sequences Using a Custom Snakemake Pipeline

Emerging viruses in the Tobamovirus genus, such as tobamo brown rugose fruit virus, pose threats to vegetable and ornamental crops due to their highly stable virions. We developed a scalable, reproducible Snakemake pipeline to analyze large-scale public datasets, enabling parallel processing and extraction of candidate contigs for further investigation. Our framework combines bioinformatics and machine learning methods to classify known and novel tobamoviral sequences, including short or partial contigs, and supports the creation of a curated catalogue of potential novel tobamoviral sequences for downstream genomic and epidemiological analyses.