bioawk ☆

« Back to VersTracker

Description:
AWK modified for biological data

Type: Formula | Latest Version: 1.0@0 | Tracked Since: Dec 17, 2025

Links: Homepage | formulae.brew.sh

Category: Developer tools

Tags: bioinformatics awk text-processing genomics cli

Install: brew install bioawk

About:
bioawk is a specialized version of the AWK text-processing utility enhanced to handle common biological file formats. It natively supports parsing FASTA, FASTQ, SAM, and GFF formats, treating them as structured tables. This allows bioinformaticians to perform complex data extraction and transformation tasks using familiar AWK syntax without pre-processing files.

Key Features:

Native parsing of FASTA, FASTQ, SAM, and GFF formats
Built-in variables like 'name', 'seq', and 'qual' for immediate access
Backward compatible with standard GNU AWK syntax
Lightweight and fast command-line execution

Use Cases:

Filtering FASTQ files by sequence length or quality score
Extracting specific headers or sequences from SAM/BAM alignment files
Converting between biological file formats using AWK one-liners

Alternatives:

seqtk – seqtk offers similar FASTA/FASTQ manipulation but focuses more on subsetting and format conversion than general text processing.
awk – Standard awk requires manual parsing of biological formats, whereas bioawk handles the structure natively.

License: HPND

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 12, 2025 6:35pm		0	VERSION_BUMP	561de740