# Install fastqc with Homebrew, apt, Nix

Quality control tool for high throughput sequence data. Version 0.12.1 via Homebrew; verified 2026-06-22. Also installable with debian: sudo apt install fastqc.

## Install

```sh
sudo av install brew:fastqc
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install fastqc
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install fastqc
```

  Evidence: Debian stable package indexes: fastqc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

- Nix (92%):

```sh
nix profile install nixpkgs#fastqc
```

  Evidence: nixpkgs package indexes: pkgs/by-name/fa/fastqc/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

## Package facts

- **Package key:** brew:fastqc
- **Package manager:** Homebrew
- **Version:** 0.12.1
- **Source summary:** Quality control tool for high throughput sequence data
- **Homepage:** <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>
- **Last updated:** 2026-06-22T14:03:18-07:00
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- fastqc (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 0.12.1
## Project history and usage

FastQC is Babraham Bioinformatics' quality-control application for high-throughput sequencing data. It analyzes FASTQ, BAM, and SAM inputs and produces graphical and HTML reports that flag unusual properties before downstream analysis.

### Project history

FastQC was created by Simon Andrews at Babraham Bioinformatics and had public releases by April 2010, according to the official project changelog. The project page describes it as stable, mature Java software released under GPL v3 or later.

The GitHub repository was created in 2017 as the public source-code home for developers and bug tracing, while the Babraham project page remains the canonical place for users to download compiled packages and read documentation.

### Adoption history

FastQC became a standard first-pass QC tool for high-throughput sequencing because it works both as an interactive GUI and as a non-interactive pipeline step. The project page emphasizes permanent HTML report export and example reports for Illumina, RNA-Seq adapter contamination, small RNA, RRBS, PacBio, and 454 datasets.

Its release history shows long maintenance from 2010 through the 0.12.x releases in 2023, adapting to new sequencing formats and operational needs such as NovaSeq tile handling, Nanopore format changes, SVG output, and memory options.

### How it is used

Users run FastQC before deeper analysis to get a quick overview of raw sequence quality. Its modules summarize base quality, sequence content, duplication, adapter content, and other signals, then mark modules as pass, warning, or fail.

FastQC can process multiple files in the graphical application, or run headlessly in pipelines to generate one report per input file. It documents no persistent package configuration file or credential store.

### Why package nerds care

FastQC is a canonical bioinformatics package-manager resident: a Java GUI that is also a CLI pipeline tool, a project website that predates the GitHub source repo, and output reports recognizable across sequencing workflows.

### Timeline

- 2010: Version 0.1 is released.
- 2017: The public GitHub source repository is created.
- 2018: v0.11.8 is released with performance and behavior fixes.
- 2023: v0.12.x releases add modern report and runtime improvements.

### Related projects

- FastQC is commonly paired with FASTQ preprocessing tools such as fastp; fastp's own README describes its HTML report as FastQC-like.

### Sources

- <https://www.bioinformatics.babraham.ac.uk/projects/fastqc>
- <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help>
- <https://github.com/s-andrews/FastQC>
- <https://github.com/s-andrews/FastQC#readme>
- <https://api.github.com/repos/s-andrews/FastQC/releases>


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Other Package-Manager Records

- Debian apt - fastqc - 0.12.1+dfsg-4: normalized package name match | Debian stable package indexes: fastqc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | quality control for high throughput sequence data | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Nix - fastqc: normalized package name match | nixpkgs package indexes: pkgs/by-name/fa/fastqc/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - fastqc - 0.12.1+dfsg-3: normalized package name match | Ubuntu 24.04 LTS package indexes: fastqc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | quality control for high throughput sequence data | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/


## Combined YAML source

View the package source record on GitHub. [combined/fastqc.yml](https://github.com/mxcl/pkgdb/blob/main/combined/fastqc.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph