fastq-tools ☆
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Description:
Small utilities for working with fastq sequence files
Type: Formula  |  Latest Version: 0.8.3@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics fastq genomics cli sequence-processing
Install: brew install fastq-tools
About:
fastq-tools provides a suite of small, efficient command-line utilities for parsing, transforming, and analyzing FASTQ files. It focuses on stream-based processing to handle large sequencing datasets without excessive memory usage. The tools are designed for bioinformaticians needing quick, scriptable operations for data cleaning and preprocessing.
Key Features:
  • Stream-based processing for low memory footprint
  • Fast sequence manipulation and filtering
  • Integration with standard Unix pipelines
  • Perl-based regular expression support via PCRE
Use Cases:
  • Filtering low-quality reads from sequencing data
  • Trimming adapters or poly-A tails from sequences
  • Converting between FASTQ formats or subsetting files
Alternatives:
  • seqtk – seqtk is a faster, C-based tool with a broader feature set, while fastq-tools offers simpler, composable utilities.
  • bioawk – bioawk extends awk for bioinformatics formats, providing more general-purpose text processing than fastq-tools' specialized commands.
License: MIT
Dependencies: pcre
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, arm64_monterey, arm64_big_sur, sonoma, ventura, monterey, big_sur, catalina, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Sep 13, 2025 6:27pm 0 VERSION_BUMP a83d4b3b
Sep 13, 2024 4:25am 0 VERSION_BUMP ea994c04
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