ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
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.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-microbial-genome-characterizationgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote 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.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-microbial-genome-characterization)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-microbial-genome-characterization"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-microbial-genome-characterization/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.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-microbial-genome-characterization"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-microbial-genome-characterization.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00239 | $0.03406 |
| Opus 5.5 | $0.00096 | $0.01362 |
| Sonnet 5.5 | $0.00048 | $0.00681 |
| Haiku 4.5 | $0.00024 | $0.00341 |
Grade A, and why
tooluniverse-microbial-genome-characterization 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 1mo ago.
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.
How it starts
The opening of the file, as written. The whole thing — 177 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Microbial Genome Assembly Characterization & QC
Discover, quality-control, and structurally map genome ASSEMBLIES for any organism using the keyless NCBI Datasets genome tools. Organism/taxon in → assembly inventory, QC metrics, and chromosome/plasmid map out.
LOOK UP, DON'T GUESS
When uncertain about an accession, assembly level, replicon count, or N50, CALL the tool. Never report assembly statistics from memory — accessions and metrics change with each RefSeq release. A live NCBI Datasets answer is always more reliable than a guess.
COMPUTE, DON'T DESCRIBE
When comparing multiple assemblies or ranking by quality, retrieve each via the tools, then write and run Python (pandas) over the returned JSON to sort, score, and tabulate. Don't describe what you would compute — execute it and report actual numbers.
When to Use This Skill
Triggers:
- "What genomes are available for [organism]?" / "Find the reference genome for [taxon]"
- "Assembly stats for GCF_000005845.2" / "What's the N50 / GC content of [accession]?"
- "How many plasmids does [strain] have?" / "List the replicons in [accession]"
- "Compare the assemblies for [species] — which is best quality?"
- "Is [accession] a complete genome or draft?"
Use Cases:
- Assembly discovery: enumerate available assemblies for a taxon, optionally only reference-grade
- Assembly QC: pull length, N50, contig count, GC%, level, RefSeq category for an accession
- Replicon mapping: list chromosomes and plasmids with their RefSeq/GenBank accessions and lengths
- Assembly comparison: rank candidate assemblies of one species by completeness and contiguity
- Reference selection: identify the designated reference/representative genome for a taxon
NOT this skill (point elsewhere):
- Gene-level orthology, synteny, conservation →
tooluniverse-comparative-genomics - Plant gene structure / annotation →
tooluniverse-plant-genomics - De novo assembly from sequencing reads → no ToolUniverse tool exists; say so
- Pure taxonomy name → lineage lookups with no genome question → use NCBI taxonomy tools directly
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.
- 1mo ago First seen · 177 lines · 239 tokens per session scan A 75eefeda1f3b
tooluniverse-microbial-genome-characterization is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 239 tokens to every session and 3,406 once invoked, about $0.0010 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 2026-09-03.
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