Install badread with Homebrew

Project links

• Homepage
• Upstream docs
• Package manager page

Commands and aliases

• badread

Project history

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.

Adoption history

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.

How it is used

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.

Why package nerds care

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.

Timeline

• 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.

Sources

• 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