install

Additional install commands

macOS

Homebrewverified · 100%

brew install breseq

local Homebrew formula metadata

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 post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 2 runtime dependencies.
Build metadata lists 3 build dependencies.

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`	cli	global executable
`gdtools`	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 generated2026-07-08

manager version0.40.1

manager updated2026-06-19

local dataok

upstreamcurrent

latest detectedv0.40.1

https://github.com/barricklab/breseq

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:breseq
Version	0.40.1
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/breseq
Homepage	https://barricklab.org/breseq
Repository	https://github.com/barricklab/breseq
Upstream docs	https://github.com/barricklab/breseq/wiki
License	GPL-2.0-or-later AND MIT AND BSD-3-Clause
Source archive	https://github.com/barricklab/breseq/archive/refs/tags/v0.40.1.tar.gz
Last updated	2026-06-19T12:30:02-07:00
Pulse	updated
Dependencies	bowtie2, r
Build dependencies	autoconf, automake, libtool
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	breseq
Version Scheme	0
Revision	0
Head Version	HEAD
Bottle Stable Root URL	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	head stable

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

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.

combined/breseq.yml

Used sources

Geiger risk classifier
Nucleus package database
av.db category and tag curation
cross-ecosystem install command graph
curated package history
package relationship graph
package version freshness
package-page enrichment

Install breseq with Homebrew