# Install bioawk with Homebrew, apt, Nix AWK modified for biological data. Version 1.0 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:bioawk ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install bioawk ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install bioawk ``` Evidence: Debian stable package indexes: bioawk from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#bioawk ``` Evidence: nixpkgs package indexes: pkgs/by-name/bi/bioawk/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:bioawk - **Package manager:** Homebrew - **Package manager page:** - **Version:** 1.0 - **Source summary:** AWK modified for biological data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** HPND - **Source archive:** - **Generated:** 2026-07-10T07:20:53+00:00 ## Executables - bioawk (cli) - bioawk (alias) ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-10 - Package-manager version: 1.0 - Local data: ok - Upstream repository: https://github.com/lh3/bioawk - Upstream latest detected: v1.0 (current) - info: No package-manager update timestamp was available. ## 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 - - - - source_facts.package-manager ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bioawk - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - bioawk - 1.0-5: normalized package name match | Debian stable package indexes: bioawk from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | extension of awk for biological sequence analysis | https://github.com/lh3/bioawk - Nix - bioawk: normalized package name match | nixpkgs package indexes: pkgs/by-name/bi/bioawk/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bioawk - 1.0-4: normalized package name match | Ubuntu 24.04 LTS package indexes: bioawk from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | extension of awk for biological sequence analysis | https://github.com/lh3/bioawk ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Database and data packages](https://www.automicvault.com/pkg/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [abpoa](https://www.automicvault.com/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [abyss](https://www.automicvault.com/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [adapterremoval](https://www.automicvault.com/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [alevin-fry](https://www.automicvault.com/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [any2fasta](https://www.automicvault.com/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [augustus](https://www.automicvault.com/pkg/brew/augustus/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [autocycler](https://www.automicvault.com/pkg/brew/autocycler/) - Shares av.db curated category or tags: bioinformatics, cli, science. - [bamtools](https://www.automicvault.com/pkg/brew/bamtools/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, data, science. - [bedops](https://www.automicvault.com/pkg/brew/bedops/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, data, science. ## Combined YAML source View the package source record on GitHub. [combined/bioawk.yml](https://github.com/automic-vault/db/blob/main/combined/bioawk.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph