microbiome-diversity-reporter

Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results.

Quality

37%

Does it follow best practices?

Impact

Pending

No eval scenarios have been run

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/Academic Writing/microbiome-diversity-reporter/SKILL.md

Quality

Discovery

40%

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 identifies a clear and distinctive scientific niche (16S rRNA diversity analysis) but lacks explicit trigger guidance ('Use when...') and could benefit from listing more specific actions and natural keyword variations. The specificity of the domain prevents conflicts but the description is too terse to help Claude reliably select it.

Suggestions

Add an explicit 'Use when...' clause, e.g., 'Use when the user asks about microbiome analysis, 16S rRNA results, amplicon sequencing diversity, or community composition metrics.'

Expand specific actions, e.g., 'Interpret Shannon index, Simpson index, Chao1 richness, UniFrac distances, PCoA/NMDS ordination plots, and rarefaction curves from 16S rRNA sequencing results.'

Include common user-facing synonyms like 'microbiome', 'gut bacteria', 'OTU tables', 'ASV tables', 'amplicon sequencing' to improve trigger term coverage.

Dimension	Reasoning	Score
Specificity	Names the domain (16S rRNA sequencing) and some actions (interpret Alpha and Beta diversity metrics), but doesn't list specific concrete actions like calculating Shannon index, generating PCoA plots, comparing community compositions, etc.	2 / 3
Completeness	Describes what it does (interpret diversity metrics) but has no explicit 'Use when...' clause or equivalent trigger guidance, which per the rubric should cap completeness at 2, and the 'what' is also not very detailed, placing this at a 1.	1 / 3
Trigger Term Quality	Includes relevant technical keywords like 'Alpha diversity', 'Beta diversity', '16S rRNA', but misses common variations users might say such as 'microbiome', 'OTU', 'ASV', 'Shannon index', 'Simpson index', 'UniFrac', 'amplicon sequencing', or 'gut bacteria'.	2 / 3
Distinctiveness Conflict Risk	The combination of '16S rRNA sequencing' with 'Alpha and Beta diversity metrics' is a very specific niche that is unlikely to conflict with other skills. This is a clearly defined scientific domain.	3 / 3
	Total	8 / 12 Passed

Implementation

35%

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

This skill is heavily padded with generic boilerplate sections (Risk Assessment, Security Checklist, Lifecycle Status, Evaluation Criteria, Response Template) that are not specific to microbiome diversity analysis and waste significant token budget. While it does provide useful concrete elements like CLI examples, parameter tables, input/output format specifications, and example JSON output, the actual domain-specific guidance for interpreting diversity metrics is thin. The workflow is generic rather than tailored to the microbiome analysis domain.

Suggestions

Remove all generic boilerplate sections (Risk Assessment, Security Checklist, Lifecycle Status, Evaluation Criteria, Response Template, Output Requirements) that Claude doesn't need and that aren't specific to microbiome diversity interpretation.

Add domain-specific interpretation guidance: what Shannon index ranges mean, how to interpret PCoA plots, what PERMANOVA p-values indicate, common pitfalls in 16S diversity analysis.

Consolidate the duplicated/circular sections ('Example Usage' referencing 'Usage', 'Implementation Details' referencing 'Workflow') into a single clear workflow with validation checkpoints specific to microbiome data (e.g., check rarefaction depth, verify sample counts match metadata).

Move the parameter table and input format specifications to a separate reference file, keeping only a quick-start example in the main skill body.

Dimension	Reasoning	Score
Conciseness	Extremely verbose and repetitive. Contains massive amounts of boilerplate (Risk Assessment, Security Checklist, Lifecycle Status, Evaluation Criteria, Response Template) that add no value for Claude. Multiple sections reference each other circularly ('See ## Usage above', 'See ## Workflow above'). The skill explains obvious concepts and includes generic templates that Claude already knows.	1 / 3
Actionability	Provides concrete CLI commands with parameters, input format examples, and example JSON output, which is useful. However, much of the 'workflow' is generic process guidance rather than domain-specific executable steps. The actual microbiome analysis logic is delegated entirely to scripts/main.py with no inline code showing how diversity metrics are computed or interpreted.	2 / 3
Workflow Clarity	The workflow section (steps 1-5) is entirely generic and not specific to microbiome diversity analysis. The 'Example run plan' provides a reasonable sequence but lacks validation checkpoints specific to the domain (e.g., verifying OTU table format, checking rarefaction depth). No feedback loops for handling common microbiome data issues like low read counts or missing samples.	2 / 3
Progressive Disclosure	References a 'references/' directory and 'references/audit-reference.md', which is good. However, the main file is a monolithic wall of text (~200+ lines) with many sections that could be split out (Risk Assessment, Security Checklist, Evaluation Criteria, Response Template are all boilerplate that bloats the main file). The circular 'See ## X above' references are confusing navigation.	2 / 3
	Total	7 / 12 Passed

Validation

90%

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 — 10 / 11 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	10 / 11 Passed

Repository: aipoch/medical-research-skills
Commit: 0b96148

Reviewed: 3 days ago

Table of Contents

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