# 使用 Homebrew, apt, dnf, MacPorts, Nix, zypper 安装 bowtie2 查看 bowtie2 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:bowtie2 ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install bowtie2 ``` 证据: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install bowtie2 ``` 证据: MacPorts ports tree: science/bowtie2/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install bowtie2 ``` 证据: Debian stable package indexes: bowtie2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install bowtie2 ``` 证据: Fedora Rawhide package metadata: bowtie2 from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#bowtie2 ``` 证据: nixpkgs package indexes: pkgs/by-name/bo/bowtie2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - zypper (92%): ```sh sudo zypper install bowtie2 ``` 证据: openSUSE Tumbleweed package metadata: bowtie2 from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst ## 软件包事实 - **软件包键:** brew:bowtie2 - **软件包管理器:** Homebrew - **版本:** 2.5.5 - **来源摘要:** Fast and sensitive gapped read aligner - **主页:** - **仓库:** - **已生成:** 2026-08-03T19:37:03+00:00 ## 可执行文件 - bowtie2 (别名) - bowtie2-align-l (别名) - bowtie2-align-s (别名) - bowtie2-build (别名) - bowtie2-build-l (别名) - bowtie2-build-s (别名) - bowtie2-inspect (别名) - bowtie2-inspect-l (别名) - bowtie2-inspect-s (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: 2.5.5 ## 项目历史与用法 Bowtie 2 is a fast, memory-efficient DNA sequencing read aligner and one of the canonical command-line tools in genomics packaging. It aligns sequencing reads to long reference genomes and emits SAM for downstream tools. ### 项目历史 Bowtie 2 followed Bowtie 1, which the manual says was released in 2009 for the shorter reads common at the time. Bowtie 2 was introduced for longer reads and newer sequencing workloads, adding gapped alignment, local alignment, flexible paired-end handling, richer mapping qualities, and a different command-line and index format. The Bowtie 2 news archive shows beta releases in 2011. The main Bowtie 2 paper, 'Fast gapped-read alignment with Bowtie 2,' appeared in Nature Methods in 2012. The public GitHub repository was created in December 2012, and the official news archive notes that the source moved to GitHub in February 2014. ### 采用历史 Bowtie 2 became a standard first-stage aligner for short-read sequencing pipelines, including variation calling, ChIP-seq, RNA-seq, bisulfite sequencing, and comparative genomics. The manual explicitly names SAMtools and GATK as downstream SAM consumers and says Bowtie 2 is tightly integrated into many other tools. Distribution is broad: the supplied package facts list Homebrew, Debian, Ubuntu, Fedora, MacPorts, Nix, and openSUSE, while the official manual highlights Bioconda and SourceForge binaries. Prebuilt genome indexes on the official site further cement it as a practical packaged tool rather than just a paper artifact. ### 使用方式 Users build or download a Bowtie 2 index for a reference genome, run `bowtie2` against FASTQ reads, and feed SAM output into downstream genomics tools. Companion commands include `bowtie2-build` for index construction and `bowtie2-inspect` for index inspection. Bowtie 2 is optimized for typical Illumina-style reads aligned to long genomes, while still handling local, end-to-end, paired-end, and very long read cases with different performance tradeoffs. ### 为什么软件包爱好者会关心 Bowtie 2 is significant because it is both research software and production infrastructure. Package maintainers care about CPU threading, index formats, bundled or external compression libraries, reproducible versions for scientific workflows, and compatibility with SAM/BAM pipelines. It is also a good example of bioinformatics packaging culture: official SourceForge releases, GitHub development, Bioconda-first scientific distribution, system packages, downloadable reference indexes, and citation-driven adoption all coexist. ### 时间线 - 2009: Bowtie 1 released for then-common short sequencing reads. - 2011: Bowtie 2 beta releases appeared in the official news archive. - 2012: Bowtie 2 paper published in Nature Methods. - 2012: Public GitHub repository created. - 2014: Official news archive announced Bowtie 2 source on GitHub. - 2018: Thread-scaling paper published for high-thread-count processors. - 2026: Bowtie 2 v2.5.5 listed as the latest official release. ### Related projects - Bowtie 1 is the predecessor for shorter, ungapped alignments. - SAMtools and GATK are downstream tools named by the manual as SAM consumers. - BWA, minimap2, STAR, and HISAT2 are related read aligners in genomics workflows. - Bioconda is a major distribution channel for scientific command-line packages including Bowtie 2. ### 来源 - - - - - ## 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 - Debian apt - bowtie2 - 2.5.4-1+b2: normalized package name match | Debian stable package indexes: bowtie2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | ultrafast memory-efficient short read aligner | https://bowtie-bio.sourceforge.net/bowtie2 - Debian apt - bowtie2-examples - 2.5.4-1: normalized package name match | Debian stable package indexes: bowtie2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Examples for bowtie2 | https://bowtie-bio.sourceforge.net/bowtie2 - Nix - bowtie2: normalized package name match | nixpkgs package indexes: pkgs/by-name/bo/bowtie2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bowtie2 - 2.5.2-1: normalized package name match | Ubuntu 24.04 LTS package indexes: bowtie2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | ultrafast memory-efficient short read aligner | https://bowtie-bio.sourceforge.net/bowtie2 - Ubuntu apt - bowtie2-examples - 2.5.2-1: normalized package name match | Ubuntu 24.04 LTS package indexes: bowtie2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Examples for bowtie2 | https://bowtie-bio.sourceforge.net/bowtie2 - dnf - bowtie2 - 2.5.4-2.fc45: normalized package name match | Fedora Rawhide package metadata: bowtie2 from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst | An ultra fast and memory-efficient read aligner | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - zypper - bowtie2 - 2.5.4-2.6: normalized package name match | openSUSE Tumbleweed package metadata: bowtie2 from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst | Fast and memory-efficient short read aligner | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - MacPorts - bowtie2: normalized package name match | MacPorts ports tree: science/bowtie2/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Combined YAML source View the package source record on GitHub. [combined/bowtie2.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bowtie2.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