# badread を Homebrew でインストール badread のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。 ## インストール ```sh sudo av install brew:badread ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install badread ``` 証拠: local Homebrew formula metadata ## パッケージ情報 - **パッケージキー:** brew:badread - **パッケージマネージャ:** Homebrew - **パッケージマネージャページ:** - **バージョン:** 0.4.2 - **ソース概要:** Long read simulator that can imitate many types of read problems - **ホームページ:** - **リポジトリ:** - **上流ドキュメント:** - **ライセンス:** GPL-3.0-or-later - **ソースアーカイブ:** - **最終更新:** 2026-04-22T09:09:57Z - **生成日時:** 2026-07-10T07:20:53+00:00 ## 実行可能ファイル - badread (cli) - badread (エイリアス) ## 依存関係 - numpy - python@3.14 - scipy ## インストール挙動 - post-install フック: 未定義 - Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## バージョンと鮮度 - ページ生成日: 2026-07-10 - マネージャ版: 0.4.2 - マネージャ更新日: 2026-04-22 - ローカルデータ: OK - 上流リポジトリ: https://github.com/rrwick/Badread - 検出された最新: v0.4.2 (最新) ## プロジェクトの歴史と使われ方 Badread is a bioinformatics CLI for simulating error-prone long sequencing reads. It is historically notable less as a large software platform and more as a citable research tool that gave developers controlled ways to stress-test long-read assemblers and analysis pipelines. ### プロジェクトの歴史 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. ### 採用の歴史 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. ### 使われ方 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. ### パッケージ好きにとっての重要性 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. ### タイムライン - 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. ### ソース - - - - - source_facts.package-manager ## セキュリティノート narrow executable package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - narrow executable package without higher-risk signals ## ソースデータベース詳細 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** badread - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 関連リンク - [Source-control packages](https://www.automicvault.com/ja/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [numpy](https://www.automicvault.com/ja/pkg/brew/numpy/) - Runtime dependency declared by Homebrew. - [python@3.14](https://www.automicvault.com/ja/pkg/brew/python-3-14/) - Runtime dependency declared by Homebrew. - [adapterremoval](https://www.automicvault.com/ja/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [alevin-fry](https://www.automicvault.com/ja/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bbtools](https://www.automicvault.com/ja/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [bowtie2](https://www.automicvault.com/ja/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [btllib](https://www.automicvault.com/ja/pkg/brew/btllib/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [cutadapt](https://www.automicvault.com/ja/pkg/brew/cutadapt/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastp](https://www.automicvault.com/ja/pkg/brew/fastp/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [fastq-tools](https://www.automicvault.com/ja/pkg/brew/fastq-tools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing. - [flye](https://www.automicvault.com/ja/pkg/brew/flye/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, long, python, python-3-14. - [kraken2](https://www.automicvault.com/ja/pkg/brew/kraken2/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, python, python-3-14, science. ## Combined YAML source View the package source record on GitHub. [combined/badread.yml](https://github.com/automic-vault/db/blob/main/combined/badread.yml) ## ソース - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - cross-ecosystem install command graph