bio-viromicslisted

# Bio Viromics Detect, classify, and QC viral contigs. ## Instructions 1. Start from `/tracking-taxonomy-updates` QuickClade domain routing when assemblies, MAGs, genomes, or contigs have not already been screened. Viral, virus-like, mixed, or low-confidence contigs enter this skill; bacterial/archaeal and eukaryotic rows stay on their domain-specific routes unless later evidence contradicts the triage. 2. Run virus detection with geNomad v1.8+ (use as primary plasmid-and-virus classifier). 3. Run CheckV v1.0.1 for completeness, contamination, and host-removal QC. 4. Infer the likely viral group from QuickClade, detection output, taxonomy hints, genome statistics, and marker/similarity evidence. 5. Search the literature for that viral group and write a short analysis playbook: typical reference sets, markers, comparative analyses, genome features, plots, and outlier signals used by scientists studying that group. 6. Choose taxonomy, clustering, phylogenetic, and comparative methods from the playbook: - For bacteriophage and prokaryotic-virus gene-sharing taxonomy: vConTACT3 v3.0 (hierarchical genus-to-order assignment, >95% ICTV agreement; supersedes vConTACT2). - For Nucleocytoviricota / giant viruses: gvclass v1.0 for genus-level classification combined with marker-gene phylogenies of NCLDV core genes. - For RNA viruses, ssDNA viruses, or other groups not well-served by vConTACT3: use group-specific markers, phylogenomics, and protein-family approaches from the