Bio viromics

Bio Viromics

Detect, classify, and QC viral contigs.

Instructions

1. Validate the pinned resource manifest and assemble the complete comparative evidence and reasoning bundle:

   uv run --no-project python skills/bio-viromics/scripts/build_viromics_evidence.py \
     viral_metrics.tsv --resources resources.json --hypotheses hypotheses.tsv \
     --reflections reflections.tsv --comparative-dir comparison/ \
     --out results/bio-viromics
   

   The driver checksum-verifies geNomad, CheckV, GVClass, and vConTACT3 database resources; requires at least five hypotheses including a technical/null explanation; requires initial, intermediate, and final reflections; and persists marker, family-copy, synteny, ncRNA, and genome-frontier evidence under schemas/evidence-bundle.schema.json.

2. 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.

3. Run virus detection with geNomad v1.8+ (use as primary plasmid-and-virus classifier).

4. Run CheckV v1.0.1 for completeness, contamination, and host-removal QC.

5. Infer the likely viral group from QuickClade, detection output, taxonomy hints, genome statistics, and marker/similarity evidence.

6. 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.

7. 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 literature playbook rather than forcing a phage-oriented workflow.

8. For prokaryotic-virus discovery, VirSorter2 v2.2.4 is a complementary detector to geNomad; combine with CheckV QC to remove false positives.

9. For each viral genome or high-quality viral contig, call genes and annotate proteins when needed, then inspect the annotation set according to the playbook rather than a fixed global feature list.

10. Compare each query viral genome to the literature-supported reference set. Report what matches expectations, what is missing, what is expanded, what is query-specific, and which patterns are likely artifacts.

11. Genome-size frontier — for each query, compute where the genome size and gene count sit within the distribution of close relatives AND the literature-reported extremes for the inferred viral group. State percentile, distance from the group median, and whether the query approaches or exceeds known record-class sizes (cite the paper that defines that record). This applies even when the query is mid-distribution — the placement itself is the finding.

12. Produce an interesting-findings table. If no strong discovery candidates are found, state that explicitly and list the literature-derived checks performed.

Quick Reference

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See docs/README.md.

Input Requirements

Prerequisites:

• Tools declared in the project's pinned Pixi environment. See docs/README.md for expected tools.
• Reference DB root: set BIO_DB_ROOT to the project or site-local database directory.
• Input contigs are available. Inputs:
• contigs.fasta
• results/taxonomy/domain_routing.tsv when available

Output

• results/bio-viromics/viral_contigs.fasta
• results/bio-viromics/domain_routing_review.tsv
• results/bio-viromics/checkv_results/
• results/bio-viromics/group_comparison_results/
• results/bio-viromics/analysis_playbook.md
• results/bio-viromics/viral_taxonomy.tsv
• results/bio-viromics/comparison_baseline.tsv
• results/bio-viromics/closest_relatives.tsv
• results/bio-viromics/viral_discovery_candidates.tsv
• results/bio-viromics/viral_feature_inventory.tsv
• results/bio-viromics/genome_size_frontier.tsv
• results/bio-viromics/viromics_report.md
• results/bio-viromics/logs/

Quality Gates

• CheckV quality thresholds meet project standards.
• Resource versions and database checksums are recorded and verified before classification.
• Marker, family-copy, synteny, and ncRNA artifacts refer to the same query/reference set and are linked to explicit hypothesis revisions.
• Contamination flags are below thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• Verify contigs.fasta is non-empty.
• QuickClade domain-routing evidence was reviewed for assembly/MAG/genome inputs, or the absence of a prior screen is corrected before final classification.
• Verify viral reference DBs exist under the reference root.
• Literature-derived analysis playbook names the inferred viral group, cited sources, standard analyses, and chosen/skipped methods.
• Chosen comparison method is appropriate for the inferred viral group; phage-oriented tools are not used for non-phage groups without literature support.
• Discovery scan covers the feature classes and outlier dimensions identified in the playbook.
• Closest-relative or reference-set context is reported for every high-quality viral genome where references are available.
• genome_size_frontier.tsv places each query in the size/gene-count distribution of close relatives and the literature-defined group extremes, with cited references.
• Report includes candidate discoveries with evidence, confidence, relative comparison, and follow-up checks, or a credible negative finding.

Examples

Example 1: Expected input layout

contigs.fasta

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.