MultiQC — Multi-Sample QC Report Aggregator

Overview

MultiQC automatically searches directories for QC log files from 150+ bioinformatics tools and aggregates statistics across all samples into a single interactive HTML report. It parses outputs from FastQC, samtools flagstat, STAR, HISAT2, Trim Galore, Salmon, Kallisto, featureCounts, Picard, GATK, and many more — eliminating the need to manually review per-sample QC files. Reports include interactive bar plots, scatter plots, heatmaps, and tables with configurable warnings and pass/fail thresholds.

When to Use

• Reviewing QC metrics across 10+ samples at once after FastQC, alignment, or quantification
• Final QC checkpoint before differential expression or variant analysis
• Sharing QC summaries with collaborators or including in publications
• Identifying batch effects, outlier samples, or failed sequencing runs
• Combining QC from multi-step pipelines (trimming → alignment → quantification) into one view
• Use FastQC directly instead for initial single-sample QC exploration
• For custom QC metrics not from standard tools, use Python/R directly; MultiQC parses tool outputs only

Prerequisites