# 使用 Homebrew, Nix 安装 breseq

查看 breseq 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。

## 安装

```sh
sudo av install brew:breseq
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install breseq
```

  证据: local Homebrew formula metadata

### Linux

- Nix (92%):

```sh
nix profile install nixpkgs#breseq
```

  证据: nixpkgs package indexes: pkgs/by-name/br/breseq/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

## 软件包事实

- **软件包键:** brew:breseq
- **软件包管理器:** Homebrew
- **版本:** 0.40.2
- **来源摘要:** Computational pipeline for finding mutations in short-read DNA resequencing data
- **主页:** <https://barricklab.org/breseq>
- **仓库:** <https://github.com/barricklab/breseq>
- **最后更新:** 2026-07-29T15:20:21Z
- **已生成:** 2026-08-03T19:37:03+00:00

## 可执行文件

- breseq (别名)
- gdtools (别名)

## 安装行为

- Bottle: 不可用

## 版本和新鲜度

- 页面生成时间: 2026-08-03
- 管理器版本: 0.40.2
## 项目历史与用法

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.

### 项目历史

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.

### 采用历史

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.

### 使用方式

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.

### 为什么软件包爱好者会关心

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.

### 时间线

- 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.

### 来源

- <https://barricklab.org/breseq>
- <https://formulae.brew.sh/api/formula/breseq.json>
- <https://github.com/barricklab/breseq>
- <https://github.com/barricklab/breseq/wiki>
- <https://raw.githubusercontent.com/barricklab/breseq/master/CITATION.cff>


## 安全说明

narrow executable package without higher-risk signals.

- **Geiger 风险:** 绿色 / 低
- narrow executable package without higher-risk signals

## 其他软件包管理器记录

- Nix - breseq: normalized package name match | nixpkgs package indexes: pkgs/by-name/br/breseq/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1


## Combined YAML source

View the package source record on GitHub. [combined/breseq.yml](https://github.com/mxcl/pkgdb/blob/main/combined/breseq.yml)


## 来源

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph