MultiQC/MultiQC

Health v2 · maintenance only

Adoption not part of the score

1489 stars · 682 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

MultiQC is a Python command-line tool that scans directories for log files and outputs from 150+ bioinformatics tools and aggregates them into a single interactive HTML report. It is designed to be run at the end of analysis pipelines to summarize quality-control statistics across many samples and analysis steps.

Use cases

• aggregate QC metrics from many sequencing samples into one report
• summarize outputs of multiple bioinformatics tools in a single HTML page
• detect outliers and batch effects across samples in an NGS pipeline
• add a final QC reporting step to a Nextflow or other genomics pipeline
• compare quality statistics across all samples without opening individual tool logs
• parse custom script outputs into a standardized report

When to choose

• you run bioinformatics pipelines with many samples and need consolidated QC reporting
• you use popular genomics tools (FastQC, Samtools, etc.) whose logs MultiQC already parses
• you want interactive, shareable HTML reports with plots and data exports

When to avoid

• your domain is not bioinformatics/genomics and no module exists for your tool outputs
• you need a real-time monitoring dashboard rather than a static report
• you need programmatic APIs for downstream processing rather than human-readable reports

Facets

cli-tool · maturity stable

data-visualization analytics parser bioinformatics data-visualization analytics developer-tools python cli cross-platform quality-control html-reports sequencing ngs genomics pipeline-reporting reporting docker

Member repositories

For agents

markdown · JSON · MCP: product_card(name="MultiQC/MultiQC")