Bio Viromics

Bio Viromics

Detect, classify, and QC viral contigs.

Instructions

Tool guides and versions: docs/README.md.

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

   uv run --script 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. Database resources may be files or directories. Set kind to directory and record the deterministic tree SHA-256 for installed database directories.

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 v1.1.1 with database v1.5 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 v3.2.4 (hierarchical genus-to-order assignment, >95% ICTV agreement; supersedes vConTACT2).
   • For Nucleocytoviricota / giant viruses: gvclass v1.6.0 with resources v1.5.0 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 and order it deterministically from genome_size_frontier.tsv. Sort by record_class in the order above_literature_max, within_known_range; then by distance_from_median descending, with blank or non-numeric values last; then by genome ascending. If no strong discovery candidates are found, state that explicitly and list the literature-derived checks performed.

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/
• stdout: the last line is one JSON envelope {ok, skill, out, manifest, warnings} (driver stdout contract in AGENTS.md)
• Artifact contract: schemas/evidence-bundle.schema.json

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 execution failure, preserve logs and report the failed command; retry only after diagnosing the cause and recording the changed parameters. Report unmet biological thresholds as results; never tune parameters solely to pass a gate.
• 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.

Non-Goals

• No host assignment beyond the evidence the run produced. Without host-linked signal from the chosen tools, the host stays unassigned.
• No completeness or contamination claims without CheckV; detector output alone does not grade a viral genome.
• No lifecycle calls (lytic, lysogenic, chronic) from sequence alone.
• No phage-oriented taxonomy for groups the literature playbook does not support, and no classification while database checksums are unverified.