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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
Additional install commands
overview
Package summary
Small utilities for working with fastq sequence files
Project links
Commands and aliases
- fastq-grep
- fastq-kmers
- fastq-match
- fastq-qscale
- fastq-qual
- fastq-qualadj
- fastq-sample
- fastq-sort
- fastq-uniq
history
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 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 13 platform targets.
- Installs with 1 runtime dependencies.
- Build metadata lists 3 build 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
| Command | Kind | Exposure | Note |
|---|---|---|---|
fastq-grep | cli | global executable | |
fastq-kmers | cli | global executable | |
fastq-match | cli | global executable | |
fastq-qscale | cli | global executable | |
fastq-qual | cli | global executable | |
fastq-qualadj | cli | global executable | |
fastq-sample | cli | global executable | |
fastq-sort | cli | global executable | |
fastq-uniq | cli | global 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 version0.8.3
manager updated
local dataok
upstreamcurrent
latest detectedv0.8.3
https://github.com/dcjones/fastq-tools
- infoNo package-manager update timestamp was available.low confidence
install metadata
Package metadata
| Package key | brew:fastq-tools |
|---|---|
| Version | 0.8.3 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/fastq-tools |
| Homepage | https://github.com/dcjones/fastq-tools |
| Repository | https://github.com/dcjones/fastq-tools |
| Upstream docs | https://github.com/dcjones/fastq-tools#readme |
| License | MIT |
| Source archive | https://github.com/dcjones/fastq-tools/archive/refs/tags/v0.8.3.tar.gz |
| Dependencies | pcre |
| Build dependencies | autoconf, automake, libtool |
| Bottle | available (on arm64_big_sur, arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, big_sur, catalina, monterey, sonoma, ventura, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | fastq-tools |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | yes |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
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.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- package relationship graph
- package version freshness
- package-page enrichment