bio-annotationlisted

# 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. Normalize tool outputs and generate the complete comparison bundle with the schema-backed driver: ```bash uv run --script skills/bio-annotation/scripts/build_annotation_artifacts.py \ raw_annotations.tsv --genomes genomes.tsv --markers marker_catalog.tsv \ --out results/bio-annotation ``` The driver refuses a non-empty destination, enforces globally unique protein identifiers, writes normalized Parquet tables, adds explicit absent-marker rows, and computes query-specific/missing/expanded/contracted families against the reference median. The artifact contract is in `schemas/artifacts.schema.json`. 3. 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. 4. 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. 5. Run InterProScan for domain/family annotation. 6. Run eggNOG-mapper v2.1.13+ for orthology-based annotation. 7. Run sequence-vs-database search and resolve taxonomy with TaxonKit v0.20.0+ (r