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tiledbvcf

Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.

55

Quality

69%

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SecuritybySnyk

Passed

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tessl review fix ./backend/cli/skills/biology/tiledbvcf/SKILL.md

The canonical home for this skill is tiledbvcf in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

50%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 core open-source content (Quick Start, CLI, Key Concepts, Pitfalls) is executable and well-organized, but the document is bloated by a large marketing-flavored TileDB-Cloud section, lacks validation checkpoints for batch ingestion, and keeps everything in one monolithic file with no progressive disclosure. Trimming the cloud promotional material into a pointed-to reference and adding post-ingest verification steps would lift the weakest dimensions.

Suggestions

Cut or compress the marketing sections ("Enterprise Features", "Cost Optimization", "Security and Compliance", "Getting Started with TileDB-Cloud", "When to Migrate Checklist") — they consume ~130 lines without actionable guidance.

Add validation checkpoints after batch ingestion, e.g. "After ingest, verify with `tiledbvcf list --uri my_dataset` and `tiledbvcf stat --uri my_dataset` before proceeding".

Move the "Scaling to TileDB-Cloud" material into a separate reference file (e.g. references/cloud.md) and link it from a short section, filling the currently empty "## Resources" heading.

DimensionReasoningScore

Conciseness

Noticeably verbose with several padded sections: ~130 lines of vendor marketing ("TileDB-Cloud provides enterprise-scale capabilities", "**End-to-End Encryption**: Data encrypted in transit and at rest", "**Start Free**: TileDB-Cloud offers free tier for evaluation", "Contact sales@tiledb.com for enterprise needs"), a redundant 10-bullet "When to Use This Skill" list, and vague capability bullets ("Maintain data provenance and metadata", "Lossless data export preserving all annotations") that instruct nothing. Not 3: the padding is substantial (roughly a third of the body), not just occasional over-explanation.

2 / 5

Actionability

Core flows are copy-paste ready: install commands ("mamba install -y -c conda-forge -c bioconda -c tiledb tiledb-py tiledbvcf-py pandas pyarrow numpy"), working ingest/query/export Python, and concrete CLI usage ("tiledbvcf store --uri my_dataset --samples sample1.vcf.gz,sample2.vcf.gz"). Not 5: the TileDB-Cloud ingestion example is explicitly hedged pseudocode ("# Note: Exact API requires TileDB-Cloud documentation") and advanced APIs like "tiledbvcf.read_allele_frequency" / "tiledbvcf.sample_qc" are unverifiable. Not 3: the bulk of the guidance is genuinely executable, covering the common cases.

4 / 5

Workflow Clarity

A sequence exists (install → create dataset → ingest → query → export) and requirements are stated ("VCFs must be single-sample", "Must have indexes: .csi (bcftools) or .tbi (tabix)"), but there are no validation checkpoints: after batch ingestion nothing tells Claude to verify (e.g., run "tiledbvcf list --uri" or "tiledbvcf stat" to confirm samples landed), and the "Common Pitfalls" list is error avoidance, not a feedback loop. Per the rubric, batch operations without validation cap this at 3.

3 / 5

Progressive Disclosure

The single 446-line file has no reference files at all, and content that clearly belongs in a separate file is inlined — notably the ~130-line "Scaling to TileDB-Cloud" section and the advanced API snippets; there is even an empty "## Resources" heading with no content beneath it. Not 2: section headers are clear and navigation within the file is easy, so structure is better than "minimal". Not 4: nothing is split out despite the size, and the empty Resources heading signals an intended-but-missing reference layout.

3 / 5

Total

12

/

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.

A specific, well-scoped description that names the tool and its concrete operations with excellent distinctiveness. Its main weakness is the missing "Use when..." trigger clause, which caps completeness, alongside slightly incomplete natural-keyword coverage (no file extensions or common synonyms).

Suggestions

Append an explicit trigger clause, e.g. "Use when working with VCF/BCF files, storing or querying variant data, or building population genomics datasets."

Add natural trigger variations and file extensions such as ".vcf", ".bcf", "variants", and "genotypes" to broaden keyword coverage.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions — "VCF/BCF ingestion", "incremental sample addition", "compressed storage", "parallel queries", and "export capabilities" — giving comprehensive coverage of the skill's operations, matching the top anchor. Not 4: there are no material gaps in the capability list.

5 / 5

Completeness

The "what" is clear ("Efficient storage and retrieval of genomic variant data using TileDB" plus named operations), but there is no "Use when..." clause; "for population genomics" only weakly implies when, so per the rubric guideline a missing explicit trigger clause caps this at 3. Not 4: the "when" is never stated explicitly.

3 / 5

Trigger Term Quality

Includes good natural terms users would say — "VCF/BCF", "genomic variant data", "population genomics" — but misses file extensions (".vcf", ".bcf") and synonyms such as "variant calling" or "genotypes", so it falls short of the comprehensive-synonyms anchor. Not 3: coverage goes well beyond "some relevant keywords".

4 / 5

Distinctiveness Conflict Risk

"TileDB" combined with "VCF/BCF" and "population genomics" carves a clear niche with distinct triggers and minimal conflict risk with other skills. Not 4: overlap with even closely related genomics skills is negligible.

5 / 5

Total

17

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/tiledbvcf/SKILL.md

Reviewed

Table of Contents

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