name: fastqc-quality-analyzer description: Sequencing quality control skill for assessing read quality, adapter contamination, and sequence composition allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • sequence-analysis
  • quality-control
  • ngs
  • qc

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)