# Install fastq-tools with Homebrew Small utilities for working with fastq sequence files. Version 0.8.3 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:fastq-tools ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install fastq-tools ``` Evidence: local Homebrew formula metadata ## Package facts - **Package key:** brew:fastq-tools - **Package manager:** Homebrew - **Package manager page:** - **Version:** 0.8.3 - **Source summary:** Small utilities for working with fastq sequence files - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - fastq-grep (cli) - fastq-kmers (cli) - fastq-match (cli) - fastq-qscale (cli) - fastq-qual (cli) - fastq-qualadj (cli) - fastq-sample (cli) - fastq-sort (cli) - fastq-uniq (cli) - fastq-grep (alias) - fastq-kmers (alias) - fastq-match (alias) - fastq-qscale (alias) - fastq-qual (alias) - fastq-qualadj (alias) - fastq-sample (alias) - fastq-sort (alias) - fastq-uniq (alias) ## Dependencies - pcre ## Build dependencies - autoconf - automake - libtool ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_big_sur, arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, big_sur, catalina, monterey, sonoma, ventura ## Freshness - Page generated: 2026-07-08 - Package-manager version: 0.8.3 - Local data: ok - Upstream repository: https://github.com/dcjones/fastq-tools - Upstream latest detected: v0.8.3 (current) - info: No package-manager update timestamp was available. ## Project history and usage fastq-tools is a compact suite of Unix-style utilities for FASTQ sequencing files, including tools for sorting, grepping, k-mer counting, local sequence matching, quality-score tabulation and adjustment, sampling, and duplicate counting. ### Project history Daniel C. Jones published fastq-tools under an MIT-style license in 2011. The README presents it as a collection of small and efficient programs for common tasks with high-throughput sequencing data in FASTQ format. The package follows the older autotools-era scientific CLI model: generated configure scripts for release tarballs, autogen.sh for git checkouts, and a short dependency list of PCRE and zlib. The GitHub repository remained active through later tags, with v0.8.3 listed among its published tags. ### Adoption history fastq-tools is niche compared with later all-in-one preprocessors, but it fills a durable command-line niche for people who want small composable tools over a single workflow application. Its Homebrew packaging reflects that Unix-toolbox use case. ### How it is used The suite works with ordinary and gzipped FASTQ files. Users pick individual commands such as fastq-sort, fastq-grep, fastq-kmers, fastq-sample, fastq-uniq, and fastq-qual rather than configuring a long-running application. No persistent configuration or credentials file is documented; behavior is driven by command-line options and the input FASTQ streams or files. ### Why package nerds care fastq-tools is significant as a small-binary, many-command package: it packages the FASTQ format as a shell-friendly toolkit. That makes it closer to classic text-processing utilities than to GUI or report-heavy bioinformatics applications. ### Timeline - 2011: The GitHub repository is created and the README copyright names Daniel C. Jones. - 2011: The project is released as a set of small FASTQ utilities. - 2022: The repository shows later maintenance activity. - 2022: v0.8.3 is listed among repository tags. ### Related projects - fastq-tools complements larger FASTQ quality-control and preprocessing tools by providing focused filters and counters for shell pipelines. ### 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:** fastq-tools - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** yes - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [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. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [pcre](https://www.automicvault.com/pkg/brew/pcre/) - Runtime dependency declared by Homebrew. - [autoconf](https://www.automicvault.com/pkg/brew/autoconf/) - Build dependency declared by Homebrew. - [automake](https://www.automicvault.com/pkg/brew/automake/) - Build dependency declared by Homebrew. - [libtool](https://www.automicvault.com/pkg/brew/libtool/) - Build dependency declared by Homebrew. - [fastp](https://www.automicvault.com/pkg/brew/fastp/) - 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. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastqc](https://www.automicvault.com/pkg/brew/fastqc/) - 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. - [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. ## Combined YAML source View the package source record on GitHub. [combined/fastq-tools.yml](https://github.com/automic-vault/db/blob/main/combined/fastq-tools.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 - cross-ecosystem install command graph