bio-annotation

Bio Annotation

Functional annotation and taxonomy inference from sequence homology.

Instructions

1. Read docs/README.md and the relevant tool guides before running anything.
2. When a nucleotide assembly, MAG, genome, or contig FASTA is available, run /tracking-taxonomy-updates first for the BBTools-container QuickClade percontig domain screen. Use that routing table to choose the right taxonomy/QC path before interpreting protein annotations.
3. For InterProScan, read docs/interproscan-usage.md and validate the exact CLI with --help or --version. Current stable is v5.77-108.0; InterProScan 6 (Nextflow-based) is a forward-looking migration target.
4. Run InterProScan for domain/family annotation.
5. Run eggNOG-mapper v2.1.13+ for orthology-based annotation.
6. Run sequence-vs-database search and resolve taxonomy with TaxonKit v0.20.0+ (required for the March 2025 NCBI rank update that replaces "superkingdom" with "domain" and adds "realm" for viruses).
   • Default CPU path: DIAMOND v2.1.20+. For any search against NCBI nr, prefer a clustered nr database (e.g., a clusterednr build under $BIO_DB_ROOT) — it is dramatically faster than full nr at comparable sensitivity for most annotation tasks. Check whether a clusterednr build is available under the reference root; if not, build one with diamond makedb from a clustered FASTA (MMseqs2/CD-HIT-reduced nr) or fall back to full nr and record the choice in the run log.
   • GPU node available (CUDA Turing or newer): MMseqs2-GPU as an alternative to DIAMOND. Published benchmark: 20× faster and ~71× cheaper per query versus 128-core CPU MMseqs2, and 177–199× faster than JackHMMER iterative search for profile-equivalent workflows (Kallenborn et al., Nature Methods 2025, DOI: 10.1038/s41592-025-02819-8). Use mmseqs easy-search or easy-taxonomy with the --gpu flag.
7. For domain-specific taxonomy after QuickClade:
   • Bacteria/Archaea -> run GTDB-Tk when genome/MAG-level sequence is available and cross-check NCBI/DIAMOND lineage assignments.
   • Viral/phage -> route to /bio-viromics; use PHROG/NCVOG markers and vConTACT3 only for phage/prokaryotic-virus contexts.
   • Giant-virus/Nucleocytoviricota -> route to /bio-viromics with GVClass and NCLDV marker-gene phylogeny.
   • Eukaryota -> use EukCC for MAG/genome QC and lineage context; avoid CheckM/GTDB-Tk assumptions.
8. For group-appropriate marker families, run HMM searches against the relevant profile libraries (Pfam, TIGRFAM, COG/arCOG, PHROG/NCVOG for viruses, eukaryotic ribosomal/structural HMMs when applicable). Use pyhmmer (Python bindings around HMMER 3.4 with native SIMD and batch-friendly APIs) by default; fall back to the HMMER CLI (hmmsearch / hmmscan) when an upstream tool requires it. The choice of profile libraries is derived from the literature-derived playbook for the inferred group.
9. Build an annotation-wide feature inventory by genome/contig and by gene family/domain/pathway.
10. Marker-gene census — from the literature-derived playbook, list the diagnostic marker / machinery categories for the inferred group (e.g., replication, transcription, translation-related such as ribosomal proteins and translation factors, packaging, capsid/structural, chromatin/SMC/topoisomerase, host-interaction). For EACH query genome and each comparison-set genome supplied, record presence and copy number per category. Save as marker_census.tsv (columns: genome, category, family_id, family_name, copy_number, evidence_source, e_value, notes). Expected-but-absent markers are first-class rows, not silent omissions.
11. Per-family copy-number matrix — build a Pfam/InterPro/HMM-family × genome integer matrix covering queries AND the supplied relatives. Persist as family_copy_number_matrix.parquet. Compute per-family fold change vs the relative median; flag query-specific families, missing-expected families, expansions, and contractions in family_expansion_candidates.tsv.
12. For exploratory work, read the literature-derived analysis playbook for the inferred organism or virus group before deciding what to flag.
13. Mine the inventory for discovery candidates relative to that playbook: expected features, missing expected features, rare or expanded families, unusual combinations, annotation/taxonomy conflicts, and high-value unknowns.
14. For specialized inputs such as viruses, organelles, symbionts, pathogens, or poorly characterized lineages, use the feature classes and outlier dimensions reported in the relevant literature rather than a fixed global checklist.
15. Rank discovery candidates by evidence strength, novelty relative to the comparison baseline, confidence, and follow-up value.

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 available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Reference DB root: set BIO_DB_ROOT to the project or site-local database directory.
• Input FASTA and reference DBs are readable. Inputs:
• proteins.faa (FASTA protein sequences).
• reference_db/ (eggNOG, InterPro, DIAMOND databases + taxdump).

Output

• results/bio-annotation/annotations.parquet
• results/bio-annotation/domain_routing.tsv
• results/bio-annotation/taxonomy.parquet
• results/bio-annotation/feature_inventory.parquet
• results/bio-annotation/marker_census.tsv
• results/bio-annotation/family_copy_number_matrix.parquet
• results/bio-annotation/family_expansion_candidates.tsv
• results/bio-annotation/discovery_candidates.tsv
• results/bio-annotation/annotation_report.md
• results/bio-annotation/logs/

Quality Gates

• Annotation hit rate and taxonomy rank coverage meet project thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• Verify proteins.faa is non-empty and amino acid encoded.
• Verify proteins.faa does not contain * stop symbols before InterProScan, or strip them deliberately.
• QuickClade domain routing was used when nucleotide assemblies/genomes were available, or the protein-only reason for skipping it is recorded.
• Verify InterProScan output options are valid: use -b or -d, never both together.
• Verify packaged InterProScan installs have been initialized with python3 setup.py -f interproscan.properties when required.
• Verify required InterProScan helper binaries are resolvable, especially ps_scan.pl, pfscan, and pfsearch.
• Run a small login-node smoke test on 1-2 proteins before submitting a large cluster job.
• Verify required reference DBs exist under the reference root.
• Domain-specific taxonomy tools match the route: GTDB-Tk for Bacteria/Archaea, /bio-viromics plus vConTACT3/GVClass as appropriate for viruses, and EukCC for Eukaryota.
• Feature inventory summarizes all annotated and unannotated proteins, not only top hits.
• marker_census.tsv covers every literature-derived marker category for the inferred group with explicit zero rows for absent markers.
• family_copy_number_matrix.parquet includes the query AND the supplied relatives, and family_expansion_candidates.tsv flags query-specific, missing-expected, expanded, and contracted families with fold-change vs the relative median.
• Discovery candidates include evidence fields: gene/protein ID, annotation source, confidence, why notable, and recommended validation.
• Discovery candidates are justified against the literature-derived playbook and comparison baseline, not only by generic keyword matches.

Examples

Example 1: Expected input layout

proteins.faa (FASTA protein sequences).
reference_db/ (eggNOG, InterPro, DIAMOND databases + taxdump).

Troubleshooting

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

Issue: InterProScan fails immediately with CLI or runtime setup errors Solution: Check docs/interproscan-usage.md for mutually exclusive output flags, * stripping, one-time setup.py initialization, and ProSite PATH requirements.

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