fastqc-report-interpreter

Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

Install with Tessl CLI

npx tessl i github:aipoch/medical-research-skills --skill fastqc-report-interpreter

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Review — 81%

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Validation — 11 / 11 Passed

Validation for skill structure

SKILL.md

Review

Evals

Evaluation results

93%

14%

RNA-seq Quality Assessment and Decision Report

Application-specific quality thresholds and issue diagnosis

Criteria

Without context

With context

Per-base quality threshold

100%

Per-sequence quality threshold

100%

N content threshold

100%

Adapter content threshold

66%

100%

Duplication RNA-seq context

66%

100%

Duplication general threshold

100%

Read-end trimming recommendation

40%

100%

Trim tool recommendation

100%

Sequence bias cause diagnosis

100%

Primer randomization recommendation

25%

50%

PASS/WARNING/FAIL status used

100%

62%

Proceed recommendation

70%

100%

Without context: $0.2919 · 2m 9s · 12 turns · 19 in / 6,212 out tokens

With context: $0.6734 · 2m 51s · 26 turns · 214 in / 9,702 out tokens

100%

Genomics Lab Multi-Sample QC Pipeline

Batch analysis and programmatic API usage

Criteria

Without context

With context

Uses FASTQCInterpreter class

100%

Uses interpret_report method

80%

100%

Produces CSV output

100%

Sample1 classified as good

100%

Sample3 classified as fail

100%

Per-base quality thresholds applied

80%

100%

Adapter content thresholds applied

80%

100%

Duplication thresholds applied

87%

100%

CSV has per-metric columns

100%

Workflow documented

100%

PASS/WARNING/FAIL terminology

90%

100%

Without context: $0.6854 · 2m 33s · 42 turns · 223 in / 9,562 out tokens

With context: $0.5710 · 1m 57s · 30 turns · 2,208 in / 6,485 out tokens

94%

ChIP-seq Pipeline QC Integration

CLI usage and ChIP-seq specific interpretation

Criteria

Without context

With context

CLI --application flag

100%

70%

CLI --input flag used

100%

62%

Adapter content classified as FAIL

100%

Adapter tool recommendation

100%

Adapter cause identified

50%

100%

Sequence bias cause identified

100%

Sequence bias recommendation

37%

100%

ChIP-seq duplication context

100%

Per-base quality passes

100%

Issues JSON has cause fields

100%

FAIL requires action

100%

Without context: $1.1107 · 4m 8s · 46 turns · 261 in / 12,918 out tokens

With context: $0.8467 · 3m 27s · 35 turns · 326 in / 11,732 out tokens

Evaluated: 1 day ago
Agent: Claude Code

Table of Contents

RNA-seq Quality Assessment and Decision Report Genomics Lab Multi-Sample QC Pipeline ChIP-seq Pipeline QC Integration

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