Bio Viromics

Detect, classify, and QC viral contigs.

Instructions

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.
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.
Run virus detection with geNomad v1.8+ (use as primary plasmid-and-virus classifier).
Run CheckV v1.0.1 for completeness, contamination, and host-removal QC.
Infer the likely viral group from QuickClade, detection output, taxonomy hints, genome statistics, and marker/similarity evidence.
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.
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.
For prokaryotic-virus discovery, VirSorter2 v2.2.4 is a complementary detector to geNomad; combine with CheckV QC to remove false positives.
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.
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.
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.
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.