tooluniverse-population-genetics

Population genetics analysis — allele frequencies (gnomAD, 1000 Genomes), Hardy-Weinberg equilibrium testing, Fst between populations, GWAS associations, evolutionary constraint scores. Use for cross-population variant comparison, ancestry-aware allele frequency lookups, and population-level evolutionary analysis.

Quality

69%

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tessl review fix ./plugin/skills/tooluniverse-population-genetics/SKILL.md

Quality

Content

48%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.

Highly actionable with concrete tool tables and executable script invocations, but the body is over-long and padded with theory Claude already knows, and lacks explicit validation feedback loops while inlining content that belongs in separate reference files.

Suggestions

Move the detailed theoretical formula sets (delta-q, drift, LD decay, heritability, F-statistics) and the catalogued 'Traps' into a separate references/ file, keeping SKILL.md to tool routing and key decision rules.

Trim explanations of concepts Claude already knows (HWE genotype expectations, Punnett-square mechanics, basic Fst definition) to one-line reminders rather than full derivations.

Add explicit validation checkpoints to the Workflow Patterns (e.g. 'verify variant_id format before gnomad_get_variant', 'check VEP response shape {data,metadata} vs {error} before parsing') to convert sequences into feedback-loop workflows.

Dimension	Reasoning	Score
Conciseness	The 363-line body extensively restates population-genetics theory and Mendelian-genetics concepts Claude already knows (HWE, Fst definitions, Punnett-square steps, Hfr mapping) with padded derivations and worked 'Trap' notes that read as a textbook rather than lean skill guidance.	2 / 5
Actionability	Provides concrete, executable guidance — a tool quick-reference table with required params, named ToolUniverse tools, exact `popgen_calculator.py --type ...` invocations, and exhortations to run `python3 -c` — with only minor gaps around full end-to-end code snippets.	4 / 5
Workflow Clarity	Workflow Patterns give labeled multi-step sequences (variant frequency, GWAS, gene characterization) and the Mendelian/Hfr frameworks are numbered, but there are no explicit validation checkpoints or validate→fix→retry feedback loops despite batch/computational operations.	3 / 5
Progressive Disclosure	Has clear section headers and one real bundled file (scripts/popgen_calculator.py, referenced with a path) but inlines large reference-style blocks (full theoretical formula sets, trap catalogs) that would be better split into separate files; references are present but not consistently signaled.	3 / 5
	Total	12 / 20 Passed

Description

90%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, concrete description that names both capabilities and explicit use triggers with low conflict risk. Minor keyword synonym coverage (e.g. user-facing phrasings like 'allele frequency lookup') is the only gap.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — 'allele frequencies (gnomAD, 1000 Genomes)', 'Hardy-Weinberg equilibrium testing', 'Fst between populations', 'GWAS associations', 'evolutionary constraint scores' — providing comprehensive, specific coverage rather than generic abstractions.	5 / 5
Completeness	Clearly answers 'what' (the enumerated analysis capabilities) and 'when' via the explicit 'Use for cross-population variant comparison, ancestry-aware allele frequency lookups, and population-level evolutionary analysis' trigger clause.	5 / 5
Trigger Term Quality	Includes natural terms a user would say (allele frequencies, GWAS, cross-population variant comparison, evolutionary analysis) plus database names, but is missing common synonyms/file forms and lay phrasings that would round out coverage.	4 / 5
Distinctiveness Conflict Risk	Occupies a clear niche (population-level variant/allele statistics with named databases and metrics) with distinct triggers unlikely to fire for unrelated skills, presenting minimal conflict risk.	5 / 5
	Total	19 / 20 Passed

Validation

100%

Warnings & errors only

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: plugin/skills/tooluniverse-population-genetics/SKILL.md
Commit: 1b02920

Reviewed: 1 day ago

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