Tracking Taxonomy Updates

Report taxonomy changes from authoritative sources with explicit versions, dates, and provenance, and assign taxonomy to sequences through a QuickClade domain screen followed by a domain-specific classifier.

SKILL_DIR is the directory that contains this SKILL.md, for example ~/.agents/skills/tracking-taxonomy-updates.

Instructions

Release and name changes

1. Fix the scope: domains, timeframe, and output type.
2. Pull release notes and current releases from the sources in reference/sources.md. The snapshots in reference/last-verified-snapshots.md are examples; re-check the sources for any "latest" claim.
3. Extract versioned changes and their impact, using stable identifiers from reference/ranks-and-identifiers.md.
4. Deliver a versioned report from reference/report-template.md with conflicts flagged.

Taxonomy assignment

1. Run QuickClade first on any assembly, MAG, SAG, isolate genome, bin set, or contig FASTA, through the BBTools container with percontig (reference/tools.md). Skip it only when the user supplies a trusted domain label and asks to skip triage. QuickClade routes; it is not the final authority.
2. Convert the QuickClade machine output into domain_routing.tsv: