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fastqc-quality-analyzer

Testing & Quality
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Sequencing quality control skill for assessing read quality, adapter contamination, and sequence composition

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How to use this skill

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I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/fastqc-quality-analyzer/SKILL.md

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FastQC Quality Analyzer Skill

Purpose

Enable sequencing quality control for assessing read quality, adapter contamination, and sequence composition metrics.

Capabilities

  • Per-base quality score analysis
  • Sequence duplication detection
  • Adapter content identification
  • GC content analysis
  • Overrepresented sequence detection
  • MultiQC report aggregation

Usage Guidelines

  • Run FastQC on all raw sequencing data
  • Review quality metrics before alignment
  • Identify samples requiring additional QC
  • Aggregate results with MultiQC for cohort overview
  • Flag samples with quality issues
  • Document QC decisions and thresholds

Dependencies

  • FastQC
  • MultiQC
  • fastp

Process Integration

  • Whole Genome Sequencing Pipeline (wgs-analysis-pipeline)
  • RNA-seq Differential Expression Analysis (rnaseq-differential-expression)
  • Long-Read Sequencing Analysis (long-read-analysis)
  • Analysis Pipeline Validation (pipeline-validation)