# Fastqc Quality Analyzer

> Sequencing quality control skill for assessing read quality, adapter contamination, and sequence composition

- Skill: `a5c-ai/fastqc-quality-analyzer` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/fastqc-quality-analyzer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/fastqc-quality-analyzer/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/fastqc-quality-analyzer

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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)