使用 Homebrew 安装 badread

项目链接

• 主页

命令和别名

• badread

项目历史

The Badread GitHub repository was created in June 2018, with the first v0.1.0 GitHub release in July 2018. The README says Badread was made to test tools that take long reads as input by letting users control read problems such as chimeras, low-quality regions, systematic basecalling errors, junk reads, random reads, adapters, glitches, and quality-score models.

Badread was published in the Journal of Open Source Software in 2019 as 'Badread: simulation of error-prone long reads' with DOI 10.21105/joss.01316. That gave the package a stable academic citation path alongside its command-line distribution.

The project continued to track long-read practice in later releases, with README examples for older Oxford Nanopore reads, newer Nanopore R10.4.1-style settings, PacBio HiFi-style reads, and configurable error and qscore models.

采用历史

Badread's adoption is mainly in computational biology workflows where developers need reproducible fake FASTQ data. Its packaging in Homebrew makes it easy for macOS bioinformatics users to install without manually cloning the repository, while the README also documents pip installation directly from GitHub.

The JOSS publication and Zenodo DOI made Badread easier to cite in papers and benchmarking notes than many informal simulator scripts. GitHub release activity from 2018 through 2026 shows a maintained niche tool rather than a frozen paper artifact.

使用方式

Typical usage is badread simulate with a reference FASTA and requested quantity, piping FASTQ output through gzip. Users tune read length, identity, error model, qscore model, adapter sequences, chimeras, glitches, junk reads, random reads, and seeds.

The README emphasizes control over realism: users can deliberately make reads very bad, pretty good, very good, or platform-like in order to test how downstream tools react.

为什么软件包爱好者会关心

Badread matters to package nerds because it is a compact example of research software that deserves normal CLI packaging: it has a paper, DOI, reproducible command-line interface, domain data models, and a long tail of users who may just need the executable in a workflow.

It also shows why scientific packages often live awkwardly between GitHub, pip, Homebrew, and citation systems: the code, docs, releases, and scholarly identity all matter.

时间线

• 2018: Badread GitHub repository created and v0.1.0 released.
• 2019: Badread published in the Journal of Open Source Software.
• 2021: v0.2.0 released.
• 2023: v0.3.0 and v0.4.0 released.
• 2026: v0.4.2 released.

Related projects

• Badread is related to long-read sequencing platforms and models such as Oxford Nanopore and PacBio.
• The README compares Badread with other long-read simulators and notes dependencies such as Edlib, NumPy, SciPy, and Matplotlib.

来源

• https://doi.org/10.21105/joss.01316
• https://github.com/rrwick/Badread
• https://github.com/rrwick/Badread/releases
• https://github.com/rrwick/Badread/wiki
• source_facts.package-manager