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pysam

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

56

Quality

66%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./skills/bio/pysam/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

65%

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

The body is actionable with strong executable examples and good key-concept coverage, but it runs long, presents workflows as unordered bullet lists without validation checkpoints, and points to reference files that are not present in the bundle.

Suggestions

Ship the four referenced documents (alignment_files.md, variant_files.md, sequence_files.md, common_workflows.md) or remove the references to avoid broken navigation.

Convert the integrated-workflow bullet lists into numbered sequences with explicit validation checkpoints (e.g., verify index exists before fetch, confirm coordinates before extraction).

Trim the "Common operations" bullet lists that merely describe capabilities, keeping only guidance Claude would not already infer.

DimensionReasoningScore

Conciseness

The body is mostly efficient and well-organized, but at ~265 lines it includes bullet lists that describe capabilities rather than instruct, and could be tightened without losing clarity.

2 / 3

Actionability

Provides executable, copy-paste-ready code for reading alignments, variants, and FASTA, plus concrete samtools/bcftools CLI calls and a try/except error-handling example.

3 / 3

Workflow Clarity

Workflows are presented as bullet lists of common operations rather than sequenced steps, and none include explicit validation checkpoints; per the guidelines, batch/destructive-context workflows without validation cap at 2.

2 / 3

Progressive Disclosure

Four reference files are clearly signaled one level deep, but the references/ directory does not exist in the bundle, so the signaled deep content is absent and the SKILL.md itself carries substantial inline detail.

2 / 3

Total

9

/

12

Passed

Description

67%

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 and occupies a distinct niche, but it leans on technical jargon and omits an explicit "Use when…" activation clause, leaving the when-to-use guidance implied rather than stated.

Suggestions

Add an explicit "Use when…" clause naming natural user phrasings (e.g., "Use when working with BAM/VCF/FASTA files, calculating sequencing coverage, or building NGS analysis pipelines").

Soften trigger terms toward language users actually say ("sequencing reads", "variant calls", "reference genomes") alongside the format abbreviations.

Keep the concrete action list but ensure the closing clause drives activation rather than just labeling the domain.

DimensionReasoningScore

Specificity

Lists multiple concrete actions — "Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage" — matching the top anchor for specific concrete actions.

3 / 3

Completeness

Clearly states what the skill does, but there is no explicit "Use when…" trigger clause — "for NGS data processing pipelines" is a domain tag, not activation guidance, which caps completeness at 2 per the guidelines.

2 / 3

Trigger Term Quality

Contains relevant domain keywords (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ) but they are technical file-format abbreviations rather than natural user phrasings, and common variations a user would say are missing.

2 / 3

Distinctiveness Conflict Risk

Occupies a clear genomic/bioinformatics file-handling niche with format-specific triggers, making it unlikely to fire for an unrelated skill.

3 / 3

Total

10

/

12

Passed

Validation

87%

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

Validation14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

referenced_paths_exist

Referenced path issues: 4 missing

Warning

Total

14

/

16

Passed

Repository
wu-yc/LabClaw
Reviewed

Table of Contents

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