tracking-taxonomy-updates
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tracking-taxonomy-updates --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Tracking Taxonomy Updates Use authoritative sources to report taxonomy changes with explicit versions, dates, and provenance. ## Instructions 1. Determine scope (domain, timeframe, output type). 2. Pull authoritative updates and release notes. 3. Extract versioned changes and impacts. 4. If assigning taxonomy for any assembly, MAG, SAG, isolate genome, bin set, or contig FASTA, start with a QuickClade first-pass domain screen through the BBTools container. Save both per-input and `percontig` results before choosing downstream tools. 5. Route from the QuickClade domain screen: - Bacteria or Archaea -> run GTDB-Tk for genome taxonomy. If the GTDB-Tk reference package is missing, set up/download it under the project/reference DB root, set `GTDBTK_DATA_PATH`, and record the release before running classification. - Viral or virus-like -> route to `/bio-viromics`; use vConTACT3 for phage/prokaryotic-virus gene-sharing taxonomy and GVClass for giant-virus/Nucleocytoviricota candidates. - Eukaryota -> run EukCC for eukaryotic MAG/genome QC and taxonomy context. - Mixed, low-confidence, or conflicting domains -> split or flag contigs for manual review before domain-specific classification
- Instructions
- Quick Reference
- Domain Triage Contract
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Update scan scope
- Troubleshooting
What does the tracking-taxonomy-updates skill do?
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tracking-taxonomy-updates --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.