# 使用 Homebrew, apt, dnf, Nix 安装 bwa 查看 bwa 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:bwa ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install bwa ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install bwa ``` 证据: Debian stable package indexes: bwa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install bwa ``` 证据: Fedora Rawhide package metadata: bwa from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#bwa ``` 证据: nixpkgs package indexes: pkgs/by-name/bw/bwa/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## 软件包事实 - **软件包键:** brew:bwa - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 0.7.19 - **来源摘要:** Burrow-Wheeler Aligner for pairwise alignment of DNA - **主页:** - **仓库:** - **上游文档:** - **许可证:** GPL-3.0-or-later AND MIT - **源码归档:** - **已生成:** 2026-07-08T18:08:21+00:00 ## 可执行文件 - bwa (cli) - bwa (别名) ## 构建依赖 - sse2neon ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-07-08 - 管理器版本: 0.7.19 - 本地数据: OK - 上游仓库: https://github.com/lh3/bwa - 检测到的最新版本: v0.7.19 (当前) - 信息: No package-manager update timestamp was available. ## 项目历史与用法 BWA, the Burrows-Wheeler Aligner, is one of the canonical command-line tools for mapping DNA sequencing reads to reference genomes. It became a standard building block in short-read genomics pipelines because it combined FM-index/Burrows-Wheeler indexing with practical performance on large mammalian references. ### 项目历史 BWA was created by Heng Li and documented through a series of algorithm publications and release notes. The current README describes three major algorithms in the package: BWA-backtrack for short Illumina reads, BWA-SW for longer sequences, and BWA-MEM as the later generally recommended algorithm for many reads longer than about 70 bp. The README points users to the GitHub source repository and SourceForge release downloads, while NEWS.md records the long-running 0.7.x series. Release notes show important maintenance milestones such as GRCh38 ALT-contig support and bwakit binaries in 0.7.11, ARM64 support in 0.7.18, and the 0.7.19 bug-fix release in 2025. ### 采用历史 BWA achieved unusually broad adoption in computational biology rather than only in general-purpose Unix packaging. The official README advertises SourceForge downloads, GitHub downloads, and BioConda install counts, and the supplied package facts show Homebrew, Debian, Ubuntu, Fedora, and Nix packaging. Its adoption is also bibliographic: the README instructs users to cite the 2009 BWA-backtrack Bioinformatics paper, the 2010 BWA-SW Bioinformatics paper, and the 2013 BWA-MEM arXiv preprint depending on which algorithm they use. ### 使用方式 A typical BWA workflow builds an FM-index with `bwa index`, then maps reads with subcommands such as `bwa mem`, `bwa aln` plus `samse` or `sampe`, or `bwa bwasw`. Output is usually SAM streamed into downstream tools such as samtools. The README now notes that BWA-MEM has been superseded for many newer workloads by minimap2 for long reads and is expected to be superseded by minibwa for short reads, while BWA-MEM2 is suggested when exact legacy BWA-MEM behavior is desired. ### 为什么软件包爱好者会关心 BWA is package-nerd significant because a single small C executable sits at the center of many genomics workflows, yet its behavior is scientifically consequential. Reproducibility often depends on the exact BWA version, algorithm, reference preparation, and SAM output details. For maintainers, BWA is also a case study in domain tooling that migrated from SourceForge-era distribution to GitHub while remaining heavily consumed through scientific package managers such as BioConda and through operating-system packages. ### 时间线 - 2009: BWA-backtrack paper is published for fast short-read alignment with the Burrows-Wheeler transform. - 2010: BWA-SW paper is published for longer reads. - 2013: BWA-MEM preprint is published and becomes the recommended algorithm for many common workloads. - 2014: BWA 0.7.11 adds GRCh38 ALT-contig support and introduces bwakit binaries. - 2017: BWA 0.7.17 is released. - 2024: BWA 0.7.18 adds ARM64 support. - 2025: BWA 0.7.19 is released as a bug-fix release. ### Related projects - minimap2 is the successor recommended by the BWA README for long reads. - BWA-MEM2 is recommended when users want faster execution while preserving legacy BWA-MEM output. - minibwa is named by the README as the expected short-read replacement. - bwakit packages BWA with associated tools and reference-building workflows for some use cases. ### 来源 - - - source_facts.package-manager ## 安全说明 narrow executable package without higher-risk signals. - **Geiger 风险:** 绿色 / 低 - narrow executable package without higher-risk signals ## 源数据库详情 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bwa - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 其他软件包管理器记录 - Debian apt - bwa - 0.7.18-1: normalized package name match | Debian stable package indexes: bwa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Burrows-Wheeler Aligner | https://bio-bwa.sourceforge.net/ - Debian apt - libbwa-dev - 0.7.18-1: normalized package name match | Debian stable package indexes: libbwa-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Burrows-Wheeler Aligner source files | https://bio-bwa.sourceforge.net/ - Nix - bwa: normalized package name match | nixpkgs package indexes: pkgs/by-name/bw/bwa/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bwa - 0.7.17-7: normalized package name match | Ubuntu 24.04 LTS package indexes: bwa from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Burrows-Wheeler Aligner | http://bio-bwa.sourceforge.net/ - Ubuntu apt - libbwa-dev - 0.7.17-7: normalized package name match | Ubuntu 24.04 LTS package indexes: libbwa-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Burrows-Wheeler Aligner source files | http://bio-bwa.sourceforge.net/ - dnf - bwa - 0.7.19-1.fc45: normalized package name match | Fedora Rawhide package metadata: bwa from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | Burrows-Wheeler Alignment tool | https://github.com/lh3/bwa ## 相关链接 - [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/zh-hans/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/zh-hans/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/zh-hans/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [lastz](https://www.automicvault.com/zh-hans/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science, sequence-alignment. - [minimap2](https://www.automicvault.com/zh-hans/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science, sequence-alignment. - [mummer](https://www.automicvault.com/zh-hans/pkg/brew/mummer/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science, sequence-alignment. - [abpoa](https://www.automicvault.com/zh-hans/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [abyss](https://www.automicvault.com/zh-hans/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science, short-reads. - [bbtools](https://www.automicvault.com/zh-hans/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science. - [blast](https://www.automicvault.com/zh-hans/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [breseq](https://www.automicvault.com/zh-hans/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science. - [diamond](https://www.automicvault.com/zh-hans/pkg/brew/diamond/) - Local package facts share a topical domain. Shared terms: aligner, alignment, bioinformatics, cli, science. ## Combined YAML source View the package source record on GitHub. [combined/bwa.yml](https://github.com/automic-vault/db/blob/main/combined/bwa.yml) ## 来源 - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph