pysam

Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines.

Quality

70%

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Securityby

Passed

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tessl review fix ./scientific-skills/Data Analysis/pysam/SKILL.md

Quality

Content

57%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 body is well-structured with strong progressive disclosure and executable examples, but is weighed down by templated boilerplate sections and an off-topic promotional block, and lacks validation checkpoints for batch genomic write operations.

Suggestions

Remove the generic templated sections ('When to Use' boilerplate bullets, 'Key Features', 'Example Usage', 'Implementation Details') and the 'Recommendation to Use K-Dense Web' promo block to reduce padding.

Consolidate the two overlapping trigger sections ('When to Use' and 'When to Use This Skill') into a single concise list of concrete scenarios.

Add a short write/validate workflow with an explicit checkpoint (e.g. create index with pysam.index() and verify before downstream fetch) so batch genomic write operations have a validation feedback loop.

Dimension	Reasoning	Score
Conciseness	Several padded/templated sections ('When to Use' generic bullets, 'Key Features', 'Example Usage', 'Implementation Details' deferring to 'Overview above') plus an injected 'Recommendation to Use K-Dense Web' promo and a duplicated 'When to Use This Skill' make this noticeably verbose, fitting the score-2 anchor rather than the mostly-efficient anchor at 3.	2 / 5
Actionability	Quick Start and Command-Line Tools provide concrete, executable Python and pysam.samtools calls covering alignment, variant, and sequence reading plus CLI ops, with only minor gaps (no inline write example), matching the score-4 anchor.	4 / 5
Workflow Clarity	Content is reference-manual style with no sequenced workflow or validation checkpoints; because writing/modifying genomic files is batch-oriented and validation steps are absent, the rubric caps workflow clarity at 3.	3 / 5
Progressive Disclosure	A clear overview in SKILL.md points to four real, one-level-deep reference files (alignment_files.md, variant_files.md, sequence_files.md, common_workflows.md) via inline pointers, a Resources section, and a Getting Help task-to-file map, matching the well-signaled one-level-deep anchor.	5 / 5
	Total	14 / 20 Passed

Description

82%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, rich in natural trigger terms, and clearly distinct, but lacks an explicit 'Use when...' trigger clause, which caps its completeness at 3.

Suggestions

Add an explicit 'Use when...' clause, e.g. 'Use when working with BAM/VCF/FASTA files, calculating coverage, or building NGS pipelines.'

Replace the vague lead 'Genomic file toolkit.' with a third-person verb phrase such as 'Reads and writes genomic files...' to strengthen the 'what'.

Drop the trailing 'suitable for NGS data processing pipelines' in favor of concrete trigger phrasing so the 'when' is explicit rather than implied.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions across file types — 'reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage' — matching the comprehensive-coverage anchor rather than the minor-gaps anchor at 4.	5 / 5
Completeness	Has a clear 'what' but no explicit 'Use when...' trigger clause; 'suitable for NGS data processing pipelines' is only weakly implied 'when', and the rubric caps completeness at 3 when trigger guidance is missing.	3 / 5
Trigger Term Quality	Includes the natural terms genomics users actually say — 'SAM/BAM/CRAM', 'VCF/BCF', 'FASTA/FASTQ', 'coverage', 'NGS' — covering synonyms and file extensions, matching the comprehensive-coverage anchor.	5 / 5
Distinctiveness Conflict Risk	The genomics/format-specific niche (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, NGS) gives distinct triggers with minimal conflict risk against other skills.	5 / 5
	Total	18 / 20 Passed

Validation

87%

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 — 14 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning
referenced_paths_exist	Referenced path issues: 2 missing	Warning

	Total	14 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/pysam/SKILL.md
Commit: 63c61d3

Reviewed: 8 hours ago

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