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scikit-bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

61

Quality

71%

Does it follow best practices?

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SecuritybySnyk

Passed

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tessl review fix ./bundled/skills/scikit-bio/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

68%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 code spanning every capability and a clearly signaled one-level reference for detailed API docs. Its weaknesses are moderate redundancy between the When-to-Use list and capability sections, and the absence of validation checkpoints in the multi-step workflows.

Suggestions

Collapse the "When to Use This Skill" bullet list into the capability sections or trim it to remove duplication with Core Capabilities, improving conciseness.

Add explicit validation/verification checkpoints to the Common Workflows (e.g. confirm counts are integers before diversity, verify tree is rooted before phylogenetic metrics) to lift workflow clarity above 3.

Slim the SKILL.md toward a quick-start overview and move extended per-capability code into references/api_reference.md to strengthen progressive disclosure.

DimensionReasoningScore

Conciseness

The body is API-focused with no concept over-explanation, but the "When to Use This Skill" bullet list duplicates the ten Core Capabilities sections, and the per-section intro sentences add trimmable padding. Above 2 because there is no severe verbosity or padding; below 4 because the redundancy is more than minor.

3 / 5

Actionability

Provides copy-paste-ready, executable Python across all ten capabilities with real API calls and parameters (e.g. skbio.DNA.read, nj(distance_matrix), alpha_diversity('shannon', counts_matrix, ids=sample_ids), permanova(..., permutations=999)) plus an install command, covering the common cases comprehensively.

5 / 5

Workflow Clarity

The Common Workflows section lists four clearly sequenced multi-step pipelines, but none include validation checkpoints or feedback loops, and several involve batch operations on tables/trees — the missing validation caps this at 3. Above 2 because the sequences are coherent and well-defined, not rough or gapped.

3 / 5

Progressive Disclosure

Clear section structure (Overview, When to Use, Core Capabilities, Best Practices) with one clearly signaled one-level-deep reference to references/api_reference.md (verified to exist) for the bulk detailed API. Below 5 because the SKILL.md itself is fairly long (~430 lines) with substantial inline code that could be slimmed toward a quick-start, leaving minor organization gaps.

4 / 5

Total

15

/

20

Passed

Description

75%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 specific, distinctive, and rich in natural technical trigger terms, clearly conveying what scikit-bio does. Its main weakness is the absence of an explicit "Use when..." trigger clause, leaving the invocation condition only weakly implied.

Suggestions

Add an explicit trigger clause, e.g. "Use when working with biological sequences, phylogenetic trees, diversity metrics, or microbiome data" to lift completeness above 3.

Include a few more natural synonyms a user might say, such as 16S, ASV/OTU, FASTQ, or BIOM, to push trigger-term coverage toward comprehensive.

Lead with a strong active verb (e.g. "Analyzes and manipulates biological data") to make the core action immediately legible.

DimensionReasoningScore

Specificity

Lists multiple specific concrete capabilities — "Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O" — giving comprehensive coverage of the toolkit's actions.

5 / 5

Completeness

Has a clear "what" (biological data toolkit with enumerated capabilities) but the "when" is only weakly implied via "for microbiome analysis" — there is no explicit "Use when..." trigger clause, which per the judging guidelines caps completeness at 3.

3 / 5

Trigger Term Quality

Good keyword coverage with natural technical terms users say ("phylogenetic trees", "UniFrac", "PERMANOVA", "PCoA", "FASTA", "Newick", "microbiome analysis") plus file formats, but missing common synonyms like 16S, ASV/OTU, FASTQ, or BIOM. Falls below 5 because several natural variations a microbiome researcher would use are absent; above 3 because coverage is clearly strong.

4 / 5

Distinctiveness Conflict Risk

Occupies a clear bioinformatics/microbiome niche with highly distinct technical triggers (PERMANOVA, UniFrac, PCoA, FASTA/Newick), making conflict with other skills minimal.

5 / 5

Total

17

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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
foryourhealth111-pixel/Vibe-Skills
Reviewed

Table of Contents

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