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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.

Quality

92%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-microbial-genome-characterization in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

81%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.

A strong, highly actionable body: exact tool invocations with real values, a clearly sequenced phase workflow with explicit selection rules, pitfall corrections, and a closing validation checklist. The main deductions are redundant trigger restating and known-concept explanation in the Interpretation Table, plus a pandas comparison step specified only in prose.

Suggestions

Drop the "When to Use This Skill" trigger list from the body — it duplicates the frontmatter description almost verbatim and saves ~20 lines.

Add a short pandas snippet (or a fourth mini worked example) for Phase 5 assembly comparison, since 'write and run Python over the returned JSON to sort, score, and tabulate' is the only common case without concrete code.

Trim the Interpretation Table entries that restate standard knowledge (assembly-level definitions, the N50 definition) down to the decision-relevant deltas, or move the worked examples to a references file to shorten the always-loaded SKILL.md.

DimensionReasoningScore

Conciseness

Sections are lean and dense, but the body re-lists triggers already in the description and the Interpretation Table explains concepts Claude largely knows (assembly-level meanings, what N50 measures, "a typical bacterial genome is 2–6 Mb"). This is minor trimmable over-explanation (4 anchor) rather than the fully lean 5 anchor, and well above the padded 3 anchor.

4 / 5

Actionability

Tool calls are fully executable with exact names, literal JSON params, and real accessions (e.g. NCBIDatasets_get_sequence_reports {"accession":"GCF_000005845.2"}), and worked examples show actual outputs. The minor gap keeping it below the copy-paste-ready-everywhere 5 anchor is Phase 5's "build a pandas table" comparison step, which has sort keys but no code snippet or worked example.

4 / 5

Workflow Clarity

Phases 0–5 are clearly sequenced with skip conditions, an explicit selection precedence list in Phase 2, a known-pitfall correction (Worked Example 2's number_of_chromosomes warning with the authoritative alternative), and a Completeness Checklist acting as an explicit pre-answer validation step. Operations are read-only NCBI queries, so no destructive/batch validation cap applies.

5 / 5

Progressive Disclosure

No bundle files exist and the single SKILL.md is well-sectioned with clear headers, so navigation is easy. However, the ~170-line body inlines the three worked examples and the full interpretation tables, which could sit in one-level-deep reference files; the under-50-line simple-skill exception does not apply. Good structure with minor organization gaps — the 4 anchor.

4 / 5

Total

17

/

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.

An exemplary description: concrete capabilities with named QC metrics, verbatim user trigger phrases including synonyms and accession formats, explicit use-when guidance, and precise boundary routing to sibling skills. No vagueness, over-claims, or padding.

DimensionReasoningScore

Specificity

Lists four concrete, verifiable actions ("Resolves an organism name or taxid to assemblies", "pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category)", "enumerates chromosomes and plasmids", "compares candidate assemblies") with named metrics — comprehensive coverage matching the top anchor, not the 4 anchor which requires minor gaps.

5 / 5

Completeness

Explicitly answers "what" with three capability sentences and "when" with a literal "Use for..." list of concrete trigger phrases — exactly the top anchor pattern; third-person voice is used throughout.

5 / 5

Trigger Term Quality

Quotes natural user phrases verbatim ("what genomes are available for [organism]", "how many plasmids does [strain] have", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs") plus synonyms and both accession formats (GCF_/GCA_), giving comprehensive natural-term coverage.

5 / 5

Distinctiveness Conflict Risk

Clear niche (assembly-level genome characterization) with distinct triggers and an explicit NOT-for clause routing overlaps to named sibling skills (tooluniverse-comparative-genomics, tooluniverse-plant-genomics) — minimal 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.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository

mims-harvard/ToolUniverse

Path

plugins/tooluniverse/skills/tooluniverse-microbial-genome-characterization/SKILL.md

Reviewed

Table of Contents

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