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tooluniverse-microbial-genome-characterization

Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enumerates chromosomes and plasmids via per-replicon sequence reports, and compares candidate assemblies on quality. Use for "what genomes are available for [organism]", "assembly stats / N50 / GC content for [GCF_/GCA_ accession]", "how many plasmids does [strain] have", "compare assemblies for [species]", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs". NOT for gene-level orthology/synteny (use tooluniverse-comparative-genomics), plant gene structure (use tooluniverse-plant-genomics), de novo assembly from raw reads (no tool exists), or taxonomy-only name/lineage lookups.

76

Quality

94%

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SKILL.md
Quality
Evals
Security

Quality

Content

88%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The content is highly actionable with executable, parameterized tool calls and a clearly phased workflow backed by a verification checklist. The main weakness is mild verbosity in the interpretive prose and a single-file structure that, while well-organized, could offload some reference material.

Suggestions

Tighten the Interpretation Table: drop definitional prose Claude already knows (e.g., what N50 is, typical bacterial genome size) and keep only the domain-specific interpretation tied to NCBI fields.

Consider moving the three Worked Examples into a references/ file (e.g., EXAMPLES.md) with a one-line pointer from SKILL.md to improve progressive disclosure and reduce inline length.

The 'COMPUTE, DON'T DESCRIBE' directive is good but generic; tie it to a concrete pandas snippet showing the Phase 5 sort-by-(level, N50, contig count) pattern so the guidance is immediately executable.

DimensionReasoningScore

Conciseness

The body is mostly efficient with concrete tool calls and minimal fluff, but the Interpretation Table and Worked Examples contain explanatory prose (e.g., defining Contig N50, what 'Complete Genome' means, typical bacterial genome size) that assumes less domain knowledge than necessary and could be trimmed. Not a 3 because it is not padded with generic concepts Claude already knows; not a 5 because some explanatory sentences could be cut.

4 / 5

Actionability

Fully executable copy-paste-ready tool invocations with exact JSON parameters appear in every phase and in three worked examples with real accessions, covering the common cases — matching the top anchor.

5 / 5

Workflow Clarity

Phases 0–5 are clearly sequenced with explicit selection heuristics (Phase 2), verification directives ('LOOK UP, DON'T GUESS', 'metadata.total_available', prefer sequence_reports over number_of_chromosomes), and a final Completeness Checklist as an explicit validation step. The operation is read-only so the destructive-cap caveat does not apply.

5 / 5

Progressive Disclosure

The body is well-organized with clear section headers (Tools, Workflow, Interpretation, Worked Examples, Limitations, Checklist) and no nested references, and no bundle files exist so all content is intentionally inline. Scored 4 rather than 5 because the skill exceeds 50 lines and the long Interpretation Table and three Worked Examples could arguably be split into reference files, leaving minor organization headroom.

4 / 5

Total

18

/

20

Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is exemplary: it states concrete capabilities in third person, gives natural-language trigger phrases, and explicitly delineates scope boundaries against sibling skills. It is comprehensive without padding.

DimensionReasoningScore

Specificity

Lists multiple concrete actions in third person — 'Resolves an organism name or taxid to assemblies', 'picks the reference/representative or best-quality assembly', 'pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category)', 'enumerates chromosomes and plasmids', 'compares candidate assemblies' — comprehensive coverage matching the top anchor.

5 / 5

Completeness

Explicitly answers both 'what' (a detailed capability inventory) and 'when' (a concrete 'Use for' trigger list with multiple example phrases), plus a 'NOT for' boundary — the strongest anchor.

5 / 5

Trigger Term Quality

The 'Use for' clause enumerates natural user phrases — 'what genomes are available for [organism]', 'assembly stats / N50 / GC content for [GCF_/GCA_ accession]', 'how many plasmids does [strain] have', 'find the reference genome for [taxon]' — covering synonyms and accessions, matching the comprehensive anchor.

5 / 5

Distinctiveness Conflict Risk

Clear niche (NCBI Datasets genome-assembly characterization) with distinct triggers, and an explicit 'NOT for' clause routing gene-level orthology, plant genomics, de novo assembly, and taxonomy-only lookups to other skills, minimizing conflict risk.

5 / 5

Total

20

/

20

Passed

Validation

100%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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