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tooluniverse-sequence-analysis

Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, ortholog discovery, and FASTQ QC + alignment workflows (Trimmomatic, BWA, samtools, coverage depth). Use for sequence retrieval, sequence comparison, FASTQ QC analysis, and read alignment pre-processing.

75

Quality

92%

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SecuritybySnyk

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SKILL.md
Quality
Evals
Security

Quality

Content

85%

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

The body is highly actionable with a well-sequenced, validated workflow and properly signaled one-level-deep references to real bundle scripts. Its main weakness is mild redundancy and inline restating of facts that dedicated lookup scripts already cover.

Suggestions

Collapse the top "TOP-OF-MIND RULE" block into a pointer to the FASTQ counter table below to remove the duplicated Trimmomatic explanation and save tokens.

Trim inline wobble rules and the peptide/foldamer helix section where the amino_acids.py / biology_facts.py scripts already provide authoritative lookup, replacing prose with a script invocation.

Move the dense Tool Parameter Quick Reference and Fallbacks tables into a bundled reference file referenced one level deep to keep SKILL.md a leaner overview.

DimensionReasoningScore

Conciseness

Mostly efficient with concrete tool tables and recipes, but includes redundancy — the "TOP-OF-MIND RULE" restates the Trimmomatic counting logic detailed later, and wobble rules and peptide/foldamer content are spelled out inline despite lookup scripts existing. It could be tightened without losing clarity.

2 / 3

Actionability

Tools are documented with required params, return-shape examples, executable recipes (e.g. the mRNA recipe and ortholog recipe), and real runnable scripts with exact invocation commands — fully copy-paste ready.

3 / 3

Workflow Clarity

A clear phased pipeline (Phases 1–6), RULE ZERO checkpoint for pre-computed results, per-phase gotchas, and an explicit counter-selection table for the risky Trimmomatic counting step provide clear sequencing with validation/feedback guidance.

3 / 3

Progressive Disclosure

The body is an overview pointing to four real bundle scripts (sequence_tools.py, amino_acids.py, biology_facts.py, translate_dna.py) via clearly signaled one-level-deep path references, with detail appropriately deferred to those files.

3 / 3

Total

11

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12

Passed

Description

100%

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, well-triggered, and complete, naming concrete capabilities and an explicit 'Use for' clause. It clearly occupies a distinct niche with low conflict risk.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — "gene/protein sequence retrieval", "nucleotide/protein search", "ortholog discovery", "FASTQ QC + alignment workflows" — alongside named sources and tools, matching the anchor for listing several specific concrete actions.

3 / 3

Completeness

It explicitly answers both what the skill does and when to use it via an explicit "Use for..." clause, satisfying the top anchor for answering what AND when with explicit triggers.

3 / 3

Trigger Term Quality

The "Use for" clause surfaces natural phrasings users would say — "sequence retrieval", "sequence comparison", "FASTQ QC analysis", "read alignment pre-processing" — giving good coverage of likely trigger language.

3 / 3

Distinctiveness Conflict Risk

The niche is clear (biological sequence analysis with NCBI/Ensembl/UniProt plus FASTQ/alignment tooling) with distinct triggers unlikely to collide with other skills.

3 / 3

Total

12

/

12

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

Table of Contents

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