使用 Homebrew, Nix 安装 breseq

项目链接

• 主页
• 仓库

命令和别名

• breseq
• gdtools

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