MultiQC

Overview

MultiQC searches a project directory for analysis logs and report files generated by a wide range of bioinformatics tools, then compiles the results into a single interactive HTML report. It supports over 150 tools including FastQC, fastp, STAR, Picard, Salmon, featureCounts, and many more. MultiQC makes it easy to compare metrics across all samples in a project at a glance.

Installation

mamba install -c bioconda multiqc

Basic Usage

Run MultiQC on an entire project directory to automatically discover and aggregate all supported report files.

# Run MultiQC on an entire project directory
multiqc /project/results/ -o /project/multiqc_report/

# Run with specific module selection and title
multiqc . --module fastqc --module star --module picard \
  --title "RNA-seq QC Report" -o qc_report/

Key Parameters

Flag / option	Description
`-o`	Output directory for the report (default: current directory).
`--module`	Run only the specified modules. Repeat for multiple modules.
`--title`	Report title shown in the HTML header.
`-f` / `--force`	Overwrite existing reports in the output directory.
`-d` / `--dirs`	Prepend sample names with the directory path for disambiguation.
`-x` / `--exclude`	Exclude specific modules from the report.
`--ignore`	Ignore files or directories matching the given glob pattern.
`-c` / `--config`	Path to a YAML configuration file for customising report behaviour.
`--flat`	Use static plot images instead of interactive plots.
`--export`	Export plot data as tab-separated files alongside the report.

Expected Output

MultiQC creates the following files in the output directory:

multiqc_report.html – an interactive HTML report with plots and tables summarising metrics from all discovered tools and samples.
multiqc_data/ – a directory containing tab-separated data files for every module, a multiqc_general_stats.txt table, and the parsed log data in JSON format.

The HTML report includes a general statistics table, per-module sections with interactive plots, and a toolbar for searching, highlighting, and hiding specific samples.