Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
# Aggregate all QC outputs in directory
multiqc results/ -o qc_report/
# Specify output name
multiqc results/ -n my_project_qc
# Include specific tools only
multiqc results/ --module fastqc --module star
MultiQC recognizes outputs from 100+ bioinformatics tools:
| Category | Tools |
|---|---|
| Read QC | FastQC, fastp, Cutadapt |
| Alignment | STAR, HISAT2, BWA, Bowtie2 |
| Quantification | featureCounts, Salmon, kallisto |
| Variant Calling | bcftools, GATK |
| Single-cell | CellRanger, STARsolo |
Create multiqc_config.yaml: