macOS
Homebrewverified · 100%
brew install breseqlocal Homebrew formula metadata
brew / rank 6416
Install breseq with Homebrew, Nix
Computational pipeline for finding mutations in short-read DNA resequencing data. Version 0.40.2 via Homebrew; verified 2026-07-29. Also installable with nix: nix profile install nixpkgs#breseq.
install
Additional install commands
Linux
Nixverified · 92%
nix profile install nixpkgs#breseqnixpkgs package indexes · pkgs/by-name/br/breseq/package.nix · source: api.github.com
overview
Package summary
Computational pipeline for finding mutations in short-read DNA resequencing data
Project links
Commands and aliases
- breseq
- gdtools
history
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 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 bottle metadata was recorded.
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 |
|---|---|---|---|
breseq | executable | indexed executable | Discovered from the local executable index. |
gdtools | executable | indexed executable | Discovered from the local executable index. |
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 generated2026-08-03
manager version0.40.2
manager updated2026-07-29
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:breseq |
|---|---|
| Version | 0.40.2 |
| Package manager | Homebrew |
| Homepage | https://barricklab.org/breseq |
| Repository | https://github.com/barricklab/breseq |
| Last updated | 2026-07-29T15:20:21Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Nix95%
breseq
nix profile install nixpkgs#breseq- normalized package name match
- Matched by: Breseq
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
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation