fastqc-quality-analyzer

# 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)