# 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 ```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 - **Package manager page:** - **Version:** 0.12.1 - **Source summary:** Quality control tool for high throughput sequence data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** GPL-3.0-or-later - **Source archive:** - **Last updated:** 2026-06-22T14:03:18-07:00 - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - fastqc (cli) - fastqc (alias) ## Dependencies - openjdk ## Install behavior - Post-install hook: not defined - Bottle: available on all ## Freshness - Page generated: 2026-07-08 - Package-manager version: 0.12.1 - Package-manager updated: 2026-06-22 - Local data: ok - Upstream repository: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - info: Release/tag comparison is only available for GitHub repositories. ## 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 - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** fastqc - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 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/ ## Related links - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Database and data packages](https://www.automicvault.com/pkg/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [openjdk](https://www.automicvault.com/pkg/brew/openjdk/) - Runtime dependency declared by Homebrew. - [fastp](https://www.automicvault.com/pkg/brew/fastp/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, quality-control, science. - [fastq-tools](https://www.automicvault.com/pkg/brew/fastq-tools/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [rasusa](https://www.automicvault.com/pkg/brew/rasusa/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [sickle](https://www.automicvault.com/pkg/brew/sickle/) - Shares av.db curated category or tags: bioinformatics, cli, fastq, science, sequencing. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fgbio](https://www.automicvault.com/pkg/brew/fgbio/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, data, high, openjdk. ## Combined YAML source View the package source record on GitHub. [combined/fastqc.yml](https://github.com/automic-vault/db/blob/main/combined/fastqc.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph