macOS
Homebrewverified · 100%
brew install fastq-toolslocal Homebrew formula metadata
brew / rank 12358
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 bottle metadata was recorded.
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 | executable | indexed executable | Discovered from the local executable index. |
fastq-kmers | executable | indexed executable | Discovered from the local executable index. |
fastq-match | executable | indexed executable | Discovered from the local executable index. |
fastq-qscale | executable | indexed executable | Discovered from the local executable index. |
fastq-qual | executable | indexed executable | Discovered from the local executable index. |
fastq-qualadj | executable | indexed executable | Discovered from the local executable index. |
fastq-sample | executable | indexed executable | Discovered from the local executable index. |
fastq-sort | executable | indexed executable | Discovered from the local executable index. |
fastq-uniq | executable | indexed executable | Discovered from the local executable index. |
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 generated2026-08-03
manager version0.8.3
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:fastq-tools |
|---|---|
| Version | 0.8.3 |
| Package manager | Homebrew |
| Homepage | https://github.com/dcjones/fastq-tools |
| Repository | https://github.com/dcjones/fastq-tools |
| Bottle | not recorded |
| Service | none declared |
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
- cross-ecosystem install command graph
- curated package history
- pkg.so package database
- pkgdb category and tag curation