macOS
Homebrewverified · 100%
brew install bioawklocal Homebrew formula metadata
brew
Install bioawk with Homebrew, apt, Nix
AWK modified for biological data. Version 1.0 via Homebrew; verified from local package data.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install bioawkDebian stable package indexes · bioawk · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#bioawknixpkgs package indexes · pkgs/by-name/bi/bioawk/package.nix · source: api.github.com
overview
Package summary
AWK modified for biological data
Project links
Commands and aliases
- bioawk
history
Project history and usage
bioawk is a small but durable bioinformatics command-line package: Brian Kernighan's awk modified to understand common genomics text formats and gzip-compressed input.
Project history
The lh3/bioawk repository was created on GitHub in January 2012 and describes the project as BWK awk modified for biological data. Its README says bioawk extends Brian Kernighan's awk with BED, GFF, SAM, VCF, FASTA/FASTQ, tab-delimited headers, gzip support through zlib, and biosequence helper functions while falling back to original awk behavior when the biological extensions are not used.
Adoption history
bioawk spread through the practical genomics command-line ecosystem rather than through a large application platform. The input package metadata lists Homebrew, Debian, Ubuntu, and Nix packages, which is exactly the distribution pattern expected for a small Unix filter that bioinformaticians drop into shell pipelines.
How it is used
Common uses include extracting fields from VCF or SAM, converting FASTA/FASTQ records, reverse-complementing sequences, and using `-c fastx`, `-c sam`, `-c vcf`, or `-c hdr` to make biological records feel like awk fields.
It is especially useful when the job is too small for a full Python or Perl script but too biological for plain awk.
Why package nerds care
bioawk is package-nerd catnip because it is not a new workflow engine or framework; it is the old Unix text-processing model with just enough domain knowledge to remove glue code. It keeps awk's one-liner culture alive inside genomics pipelines.
Timeline
- 2012: lh3/bioawk repository created on GitHub.
- 2012: v1.0 tag published in the repository.
- 2010s: Packaged by Unix-like distributions for bioinformatics shell workflows.
Related projects
- bioawk is directly related to BWK awk, zlib, and command-line genomics tools such as samtools, bcftools, BED/GFF utilities, and FASTA/FASTQ pipeline filters.
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 6 platform targets.
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 |
|---|---|---|---|
bioawk | 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 generated2026-07-10
manager version1.0
manager updated
local dataok
upstreamcurrent
latest detectedv1.0
- infoNo package-manager update timestamp was available.low confidence
install metadata
Package metadata
| Package key | brew:bioawk |
|---|---|
| Version | 1.0 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/bioawk |
| Homepage | https://github.com/lh3/bioawk |
| Repository | https://github.com/lh3/bioawk |
| Upstream docs | https://github.com/lh3/bioawk#readme |
| License | HPND |
| Source archive | https://github.com/lh3/bioawk/archive/refs/tags/v1.0.tar.gz |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, 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 | bioawk |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
bioawk 1.0-5
extension of awk for biological sequence analysis
sudo apt install bioawk- Section: science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Bioawk
Nix95%
bioawk
nix profile install nixpkgs#bioawk- normalized package name match
- Matched by: Bioawk
Ubuntu apt95%
bioawk 1.0-4
extension of awk for biological sequence analysis
sudo apt install bioawk- Section: universe/science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Bioawk
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
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment