# Install breseq with Homebrew Computational pipeline for finding mutations in short-read DNA resequencing data. Version 0.40.1 via Homebrew; verified 2026-06-19. ## Install ```sh sudo av install brew:breseq ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install breseq ``` Evidence: local Homebrew formula metadata ## Package facts - **Package key:** brew:breseq - **Package manager:** Homebrew - **Package manager page:** - **Version:** 0.40.1 - **Source summary:** Computational pipeline for finding mutations in short-read DNA resequencing data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** GPL-2.0-or-later AND MIT AND BSD-3-Clause - **Source archive:** - **Last updated:** 2026-06-19T12:30:02-07:00 - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - breseq (cli) - gdtools (cli) - breseq (alias) - gdtools (alias) ## Dependencies - bowtie2 - r ## Build dependencies - autoconf - automake - libtool ## 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: 2026-07-08 - Package-manager version: 0.40.1 - Package-manager updated: 2026-06-19 - Local data: ok - Upstream repository: https://github.com/barricklab/breseq - Upstream latest detected: v0.40.1 (current) ## Project history and usage breseq is a command-line microbial genomics pipeline for finding mutations in short-read resequencing data against a reference genome. It is associated with the Barrick Lab and is aimed especially at haploid microbial genomes, with companion tooling such as gdtools for working with GenomeDiff-style results. ### Project history The project predates its 2015 GitHub import: its official citation file points users to a 2014 Methods in Molecular Biology article on identifying mutations in laboratory-evolved microbes with breseq, and to a 2014 BMC Genomics article on structural variation in haploid microbial genomes. The repository was created on GitHub in March 2015, with release v0.26.0 published shortly afterward. breseq's documentation culture is unusually deep for a packaged CLI: the official wiki is a user manual with installation material, usage pages for breseq and gdtools, and tutorials for clones, populations, barcoded/targeted data, and curation workflows. The Barrick Lab homepage also links example output and tutorial data, reflecting its origin as a research-lab tool rather than a general developer utility. ### Adoption history Adoption is strongest in microbial evolution and resequencing workflows. Official project materials point users to GitHub releases and Bioconda, while Homebrew packages it for macOS and Linux users who want a system package. Homebrew analytics reported hundreds of installs over the prior year at lookup time, a niche but steady signal for a scientific command-line package. ### How it is used Users run breseq on short-read resequencing data to call mutations relative to a reference sequence, then use its HTML reports, GenomeDiff output, and gdtools utilities to inspect, compare, or curate results. The tool is especially relevant when experiments produce many evolved microbial clones or populations that need consistent mutation calling. ### Why package nerds care For package nerds, breseq is a good example of research software that became a reproducible CLI package across multiple scientific distribution channels. It brings a citation-backed bioinformatics workflow, native C++ code, test data, tutorials, and platform packaging into the same ecosystem, which is exactly the kind of messy but valuable scientific tool package managers preserve. ### Timeline - 2014: Preferred breseq methods article and related BMC Genomics article published. - 2015: GitHub repository created and v0.26.0 release published. - 2016-2017: 0.27 through 0.30 releases continued the public release series. - 2024: v0.39.0 released. - 2026: v0.40.1 released and Homebrew stable version reported as 0.40.1. ### Related projects - gdtools is shipped with breseq for GenomeDiff manipulation and downstream analysis. - Bioconda distributes breseq for scientific package-management workflows, alongside Homebrew packaging for general Unix-like developer environments. - The Barrick Lab tutorial data and example outputs are part of the practical ecosystem around the tool. ### Sources - - - - - ## 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:** breseq - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Related links - [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. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [bowtie2](https://www.automicvault.com/pkg/brew/bowtie2/) - Runtime dependency declared by Homebrew. - [r](https://www.automicvault.com/pkg/brew/r/) - Runtime dependency declared by Homebrew. - [autoconf](https://www.automicvault.com/pkg/brew/autoconf/) - Build dependency declared by Homebrew. - [automake](https://www.automicvault.com/pkg/brew/automake/) - Build dependency declared by Homebrew. - [libtool](https://www.automicvault.com/pkg/brew/libtool/) - Build dependency declared by Homebrew. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [jellyfish](https://www.automicvault.com/pkg/brew/jellyfish/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [lastz](https://www.automicvault.com/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [minimap2](https://www.automicvault.com/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [mummer](https://www.automicvault.com/pkg/brew/mummer/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [bioperl](https://www.automicvault.com/pkg/brew/bioperl/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://www.automicvault.com/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [polypolish](https://www.automicvault.com/pkg/brew/polypolish/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, read, science. ## Combined YAML source View the package source record on GitHub. [combined/breseq.yml](https://github.com/automic-vault/db/blob/main/combined/breseq.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 - cross-ecosystem install command graph