What is tracking-taxonomy-updates?

A guide for following changes in how organisms are named and classified across major biological classification systems. It also helps route genome and sequence data to suitable classification tools.

Comparing taxonomy releases, resolving renamed organisms, and assigning genomes, genome bins, or sequence fragments to bacterial, archaeal, viral, or eukaryotic groups.

Taxonomy releases can rename organisms, change their group, or disagree across systems. This keeps comparisons tied to versions and helps flag uncertain or mixed results.

tracking-taxonomy-updates — Skill for Claude Code by fmschulz

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add fmschulz/omics-skills --skill tracking-taxonomy-updates

Clone the repo

git clone --depth 1 https://github.com/fmschulz/omics-skills

Made for: Claude Code.

Or install omics-skills, the plugin that ships this one along with the rest of its 34 skills, 4 agents.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/fmschulz/omics-skills/tracking-taxonomy-updates/github.svg)](https://agentmods.dev/skills/fmschulz/omics-skills/tracking-taxonomy-updates)

Your own site

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/tracking-taxonomy-updates"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/tracking-taxonomy-updates/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/tracking-taxonomy-updates"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/tracking-taxonomy-updates.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 51 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,469 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00051	$0.01469
Opus 5.5	$0.00020	$0.00588
Sonnet 5.5	$0.00010	$0.00294
Haiku 4.5	$0.00005	$0.00147

Measured 23d ago against content hash 3fcb2f162c84, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

tracking-taxonomy-updates scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 23d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/quickclade_to_routing.py, scripts/submit_taxonomy.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/tracking-taxonomy-updates/SKILL.md · 93 lines

How it starts

The opening of the file, as written. The whole thing — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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

Fix the scope: domains, timeframe, and output type.
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.
Extract versioned changes and their impact, using stable identifiers from reference/ranks-and-identifiers.md.
Deliver a versioned report from reference/report-template.md with conflicts flagged.

Taxonomy assignment

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.

Convert the QuickClade machine output into domain_routing.tsv:

uv run --script "$SKILL_DIR/scripts/quickclade_to_routing.py" \
  results/taxonomy/quickclade_percontig.tsv \
  --sample-id S1 --output results/taxonomy/domain_routing.tsv

Route each row:
- Bacteria or Archaea: GTDB-Tk. If the reference package is missing, install it under the project or shared database root, set GTDBTK_DATA_PATH, record the release, and pass gtdbtk check_install before classifying.
- Phage or prokaryotic virus: /bio-viromics, then vConTACT3.
- Giant virus or Nucleocytoviricota: /bio-viromics, then GVClass plus a marker-gene phylogeny.
- Eukaryota: EukCC.
- Mixed, low-confidence, or conflicting domains: split or flag the contigs for manual review before any domain-specific tool.
Submit GTDB-Tk, EukCC, vConTACT3, and GVClass through the scheduler, never on a login node:

Read the full file on GitHub · 93 lines

Files

What ships with it

10 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

23d ago Changed · -14 lines · -2 tokens per session 3fcb2f162c84
1mo ago Changed d3190428b32a
1mo ago First seen · 107 lines · 53 tokens per session scan A 183bffb5a686

Subscribe to this mod's changes

tracking-taxonomy-updates is a skill published in the GitHub repository fmschulz/omics-skills (11 stars, last pushed 23d ago), licensed MIT. It adds 51 tokens to every session and 1,469 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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