# MultiQC/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Repository: https://github.com/MultiQC/MultiQC
Canonical: https://ross.abutalabs.com/products/multiqc
Homepage: https://seqera.io/multiqc/
Language: JavaScript
License: GPL-3.0
License Family: copyleft
Topics: bioinformatics, analysis, pypi, bioconda, multiqc, python, data-visualization, quality-control, reporting, seqera, vizualisation
Last push: 2026-08-12T02:59:28+00:00

## Health v2 (maintenance only)
Score: 88/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 97, release rhythm 71, longevity 100
- inputs: {"age_days": 4047, "days_push": 21, "days_rel": 113, "gap_med": 44, "n_releases_24m": 14}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1489, forks 682 (observed 2026-08-28T04:04:52.230246+00:00)

## What it is
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
- artifact type: cli-tool
- maturity: stable
- function: data-visualization, analytics, parser
- domain: bioinformatics, data-visualization, analytics, developer-tools
- platform: python, cli, cross-platform
- tags: quality-control, html-reports, sequencing, ngs, genomics, pipeline-reporting, reporting, docker

## Member repositories
- MultiQC/MultiQC (main) score 88

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:04:52.230246+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T04:33:39.237986+00:00, confidence not recorded.
  - readme: https://github.com/MultiQC/MultiQC (fetched 2026-08-28T04:04:52.230246+00:00, sha b257039ee7db)
  - homepage: https://seqera.io/multiqc/ (fetched 2026-08-29T11:40:07.039682+00:00, sha 59f2423a74bb)
  - site_page: https://docs.seqera.io/multiqc (fetched 2026-08-29T11:40:07.049415+00:00, sha 2570efdcf471)
  - site_page: https://docs.seqera.io/multiqc/getting_started/installation?__hstc=137570287.8b28b24391ce7439150445b248bd1fbe.1722334630307.1728556007222.1728559721540.55&__hssc=137570287.1.1728559721540&__hsfp=1805135621 (fetched 2026-08-29T11:40:07.052217+00:00, sha 7f9b61e44f67)
  - site_page: https://docs.seqera.io/ (fetched 2026-08-29T11:40:07.057813+00:00, sha a93c57af9da0)
  - site_page: https://seqera.io/about (fetched 2026-08-29T11:40:07.059773+00:00, sha 9392f358e8f7)
  - site_page: https://seqera.io/pricing (fetched 2026-08-29T11:40:07.055557+00:00, sha 8993025d09d8)
- Data as of 2026-08-30T08:39:29.467469+00:00.