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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.

72

Quality

87%

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SKILL.md
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Quality

Content

75%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 highly actionable, well-sequenced tool-calling skill with executable examples and a useful completeness checklist. Its main weakness is conciseness: the Interpretation Table re-explains standard genomics concepts Claude already knows, and the long worked-example section could be split into a reference file.

Suggestions

Trim the Interpretation Table to the non-obvious gotchas only (number_of_chromosomes counts plasmids, GCF-over-GCA preference, pagination via metadata.total_available); drop basic definitions of N50, GC%, and assembly-level meanings that Claude already knows.

Move the three Worked Examples into a references/ file (e.g. examples.md) and keep one short canonical example inline, improving both conciseness and progressive_disclosure.

Add a brief error-recovery note for the workflow (what to do when suggest_taxonomy returns no matches or an accession is not found) to close the workflow_clarity validation gap.

DimensionReasoningScore

Conciseness

Mostly efficient, but the 'Interpretation Table' over-explains standard bioinformatics concepts Claude already knows ('Contig N50: the contig length at which 50% of the assembly is in contigs >= that size', definitions of Complete Genome/Chromosome/Scaffold/Contig); not the 4 anchor because the padding is noticeable rather than minor, not the 2 anchor because much of the content (GCF-vs-GCA preference, the number_of_chromosomes gotcha, pagination) genuinely earns its place.

3 / 5

Actionability

Fully executable tool calls with exact JSON params throughout (e.g. NCBIDatasets_list_genomes_by_taxon {"taxon":"562","limit":5,"reference_only":true}) and three worked examples with real accessions and actual returned metrics; not the 4 anchor because examples are copy-paste ready and cover the common cases rather than having minor gaps.

5 / 5

Workflow Clarity

Clear Phase 0-5 sequence plus a 'Completeness Checklist' acting as a pre-answer validation checkpoint; not the 5 anchor because there is no explicit error-recovery feedback loop for tool failures (e.g. empty suggest_taxonomy results, missing accession), and not the 3 anchor because the checklist supplies a real checkpoint and the read-only nature means the destructive-operation cap does not apply.

4 / 5

Progressive Disclosure

Well-organized into clear sections (Tools, Workflow, Interpretation, Examples, Limitations, Checklist) with no nested references and no bundle files present; not the 5 anchor because the three worked examples and the Interpretation Table are substantial inlined content that could live in one-level-deep reference files to shorten the core, and not the 3 anchor because sectioning is clear and nothing is buried.

4 / 5

Total

16

/

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.

A strong, third-person description that concretely lists capabilities, provides comprehensive natural trigger phrases, and explicitly routes away from sibling skills. It fully answers both what the skill does and when to use it with no vague padding.

DimensionReasoningScore

Specificity

Lists multiple concrete 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 on quality' — with comprehensive coverage; not the 4 anchor because coverage is broad and concrete rather than having only minor gaps.

5 / 5

Completeness

Explicitly answers both what ('Genome-ASSEMBLY discovery, QC, and replicon mapping') and when ('Use for ...' with concrete trigger phrases), matching the 5 anchor; not the 4 anchor because both what and when are explicit and concrete rather than only weakly specified.

5 / 5

Trigger Term Quality

Six quoted natural trigger phrases ('what genomes are available for [organism]', 'how many plasmids does [strain] have', 'find the reference genome for [taxon]') plus accession forms GCF_/GCA_ cover synonyms and concrete identifier forms users would actually say; not the 4 anchor because natural-term coverage is comprehensive rather than missing a few.

5 / 5

Distinctiveness Conflict Risk

Clear niche (NCBI Datasets genome assemblies) with explicit 'NOT for ...' routing to sibling skills (tooluniverse-comparative-genomics, tooluniverse-plant-genomics), giving minimal conflict risk; not the 4 anchor because boundaries are explicitly stated rather than leaving minor overlap.

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

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