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brew

Install fastqc with Homebrew, apt, Nix

Quality control tool for high throughput sequence data. Version 0.12.1 via Homebrew; verified 2026-06-22.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install fastqc

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install fastqc

Debian stable package indexes · fastqc · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#fastqc

nixpkgs package indexes · pkgs/by-name/fa/fastqc/package.nix · source: api.github.com

overview

Package summary

Quality control tool for high throughput sequence data

Commands and aliases

  • fastqc

history

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.

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 1 platform targets.
  • Installs with 1 runtime dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
fastqccliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08
manager version0.12.1
manager updated2026-06-22
local dataok
upstreamnot checked
latest detectednot detected

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

install metadata

Package metadata

Package keybrew:fastqc
Version0.12.1
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/fastqc
Homepagehttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Repositoryhttps://github.com/s-andrews/FastQC
Upstream docshttps://www.bioinformatics.babraham.ac.uk/projects/fastqc
LicenseGPL-3.0-or-later
Source archivehttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
Last updated2026-06-22T14:03:18-07:00
Pulseupdated
Dependenciesopenjdk
Bottleavailable (on all)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namefastqc
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

fastqc 0.12.1+dfsg-4

quality control for high throughput sequence data

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

sudo apt install fastqc
  • Section: science
  • Architecture: all
  • 5 dependencies
  • normalized package name match
  • Matched by: Fastqc
Debian stable package indexes · deb.debian.org · Debian stable package indexes: fastqc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

fastqc

nix profile install nixpkgs#fastqc
  • normalized package name match
  • Matched by: Fastqc
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/fa/fastqc/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

fastqc 0.12.1+dfsg-3

quality control for high throughput sequence data

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

sudo apt install fastqc
  • Section: universe/science
  • Architecture: all
  • 6 dependencies
  • normalized package name match
  • Matched by: Fastqc
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: fastqc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • openjdkRuntime dependency declared by Homebrew.

Same workflow

  • fastpShares av.db curated category or tags: bioinformatics, cli, fastq, quality-control, science.
  • fastq-toolsShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • rasusaShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • sickleShares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing.
  • adapterremovalShares av.db curated category or tags: bioinformatics, cli, science, sequencing.
  • alevin-fryShares av.db curated category or tags: bioinformatics, cli, science, sequencing.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment