# 使用 Homebrew, apt, MacPorts, Nix 安装 bedtools

查看 bedtools 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:bedtools
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install bedtools
```

  证据: local Homebrew formula metadata

- MacPorts (94%):

```sh
sudo port install bedtools
```

  证据: MacPorts ports tree: science/bedtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

### Linux

- Debian apt (92%):

```sh
sudo apt install bedtools
```

  证据: Debian stable package indexes: bedtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

- Nix (92%):

```sh
nix profile install nixpkgs#bedtools
```

  证据: nixpkgs package indexes: pkgs/by-name/be/bedtools/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:bedtools
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/bedtools>
- **版本:** 2.31.1
- **来源摘要:** Tools for genome arithmetic (set theory on the genome)
- **主页:** <https://github.com/arq5x/bedtools2>
- **仓库:** <https://github.com/arq5x/bedtools2>
- **上游文档:** <https://bedtools.readthedocs.io/en/latest>
- **许可证:** MIT
- **源码归档:** <https://github.com/arq5x/bedtools2/archive/refs/tags/v2.31.1.tar.gz>
- **已生成:** 2026-07-08T07:18:31+00:00

## 可执行文件

- annotateBed (cli)
- bamToBed (cli)
- bamToFastq (cli)
- bed12ToBed6 (cli)
- bedToBam (cli)
- bedToIgv (cli)
- bedpeToBam (cli)
- bedtools (cli)
- closestBed (cli)
- clusterBed (cli)
- complementBed (cli)
- coverageBed (cli)
- expandCols (cli)
- fastaFromBed (cli)
- flankBed (cli)
- genomeCoverageBed (cli)
- getOverlap (cli)
- groupBy (cli)
- intersectBed (cli)
- linksBed (cli)
- mapBed (cli)
- maskFastaFromBed (cli)
- mergeBed (cli)
- multiBamCov (cli)
- multiIntersectBed (cli)
- nucBed (cli)
- pairToBed (cli)
- pairToPair (cli)
- randomBed (cli)
- shiftBed (cli)
- shuffleBed (cli)
- slopBed (cli)
- sortBed (cli)
- subtractBed (cli)
- tagBam (cli)
- unionBedGraphs (cli)
- windowBed (cli)
- windowMaker (cli)
- annotateBed (别名)
- bamToBed (别名)
- bamToFastq (别名)
- bed12ToBed6 (别名)
- bedToBam (别名)
- bedToIgv (别名)
- bedpeToBam (别名)
- bedtools (别名)
- closestBed (别名)
- clusterBed (别名)
- complementBed (别名)
- coverageBed (别名)
- expandCols (别名)
- fastaFromBed (别名)
- flankBed (别名)
- genomeCoverageBed (别名)
- getOverlap (别名)
- groupBy (别名)
- intersectBed (别名)
- linksBed (别名)
- mapBed (别名)
- maskFastaFromBed (别名)
- mergeBed (别名)
- multiBamCov (别名)
- multiIntersectBed (别名)
- nucBed (别名)
- pairToBed (别名)
- pairToPair (别名)
- randomBed (别名)
- shiftBed (别名)
- shuffleBed (别名)
- slopBed (别名)
- sortBed (别名)
- subtractBed (别名)
- tagBam (别名)
- unionBedGraphs (别名)
- windowBed (别名)
- windowMaker (别名)

## 依赖

- xz

## macOS 提供的库

- bzip2

## 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: 2.31.1
- 本地数据: OK
- 上游仓库: https://github.com/arq5x/bedtools2
- 检测到的最新版本: v2.31.1 (当前)
- 信息: No package-manager update timestamp was available.
## 项目历史与用法

bedtools is one of the standard command-line toolkits for genome arithmetic: set-theory style operations over BED, BAM, GFF/GTF, VCF, and related genomic interval data.

### 项目历史

Aaron Quinlan first created bedtools in spring 2009 to answer genomics questions that were too slow or awkward with existing web tools and locally installed UCSC/Kent utilities. The official overview says the initial public version appeared in spring 2009 and originally supported only 6-column BED files.

The project was described in the 2010 Bioinformatics paper 'BEDTools: a flexible suite of utilities for comparing genomic features.' The toolkit later expanded beyond BED to support BAM alignments, GFF, blocked BED, and VCF, while keeping the command-line pipeline model.

The modern bedtools2 GitHub repository was created in December 2013. The README describes bedtools as the 'swiss army knife for genome arithmetic' and says it is maintained by the Quinlan Laboratory at the University of Virginia.

### 采用历史

The supplied metadata shows bedtools packaged across Homebrew, Debian, Ubuntu, MacPorts, Nix, and other distribution indexes, reflecting broad adoption as a default genomics CLI dependency.

bedtools adoption is also visible in downstream tooling: the README asks users to cite pybedtools separately, and the docs emphasize combining bedtools operations with Unix pipes for more sophisticated analyses.

### 使用方式

Common bedtools workflows include intersecting intervals, merging nearby features, computing coverage, extracting FASTA sequence, shuffling or randomizing intervals, generating genome coverage, mapping summaries over overlaps, and converting between BAM, BED, FASTQ, and other formats.

The toolkit is designed for shell composition. The official overview highlights stdin support so users can stream multiple commands together and control exactly how overlap results are reported.

### 为什么软件包爱好者会关心

bedtools is package-nerd significant because it is a canonical scientific Unix package: a suite of many small executables, stable command names, text formats, manpage-like docs, and enormous downstream workflow dependence.

It also demonstrates the tension package managers handle for research software: upstream users expect old command aliases such as intersectBed and newer unified bedtools subcommands, while distributions need reproducible builds for C++ genomics tooling that is commonly used in pipelines and papers.

In the bioinformatics package graph, bedtools is not just an application; it is infrastructure. Other tools, workflow examples, papers, and wrappers often assume it exists on PATH.

### 时间线

- 2009: Initial public version released in spring 2009.
- 2010: BEDTools paper published in Bioinformatics.
- 2013: bedtools2 GitHub repository created.
- 2021: v2.30.0 release published.
- 2023: v2.31.1 release published.

### Related projects

- BEDOPS is a close peer focused on sorted-data performance, Starch compression, and scalable interval operations.
- pybedtools wraps bedtools functionality for Python users and has its own Bioinformatics citation.
- UCSC Genome Browser, Galaxy, and Kent source utilities are named in the official overview as predecessor tools that shaped bedtools' motivation.

### 来源

- <https://api.github.com/repos/arq5x/bedtools2>
- <https://bedtools.readthedocs.io/en/latest/content/overview.html>
- <https://github.com/arq5x/bedtools2#readme>
- <https://github.com/arq5x/bedtools2/releases>
- source_facts.package-manager


## 安全说明

infrastructure mutation or orchestration signal.

- **Geiger 风险:** orange / 中
- infrastructure mutation or orchestration signal

## 源数据库详情

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** bedtools
- **Version Scheme:** 0
- **Revision:** 0
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** stable

## 其他软件包管理器记录

- Debian apt - bedtools - 2.31.1+dfsg-2: normalized package name match | Debian stable package indexes: bedtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | suite of utilities for comparing genomic features | https://github.com/arq5x/bedtools2
- Debian apt - bedtools-test - 2.31.1+dfsg-2: normalized package name match | Debian stable package indexes: bedtools-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | test data for the bedtools package | https://github.com/arq5x/bedtools2
- Nix - bedtools: normalized package name match | nixpkgs package indexes: pkgs/by-name/be/bedtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - bedtools - 2.31.1+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: bedtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | suite of utilities for comparing genomic features | https://github.com/arq5x/bedtools2
- Ubuntu apt - bedtools-test - 2.31.1+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: bedtools-test from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | test data for the bedtools package | https://github.com/arq5x/bedtools2
- MacPorts - bedtools: normalized package name match | MacPorts ports tree: science/bedtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1


## 相关链接

- [Source-control packages](https://www.automicvault.com/zh-hans/pkg/source-control-tools/) - Belongs to a source-control command family.
- [Secret-risk packages](https://www.automicvault.com/zh-hans/pkg/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals.
- [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.
- [xz](https://www.automicvault.com/zh-hans/pkg/brew/xz/) - Runtime dependency declared by Homebrew.
- [autocycler](https://www.automicvault.com/zh-hans/pkg/brew/autocycler/) - Shares av.db curated category or tags: bioinformatics, cli, genome, science.
- [abpoa](https://www.automicvault.com/zh-hans/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [abricate](https://www.automicvault.com/zh-hans/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [abyss](https://www.automicvault.com/zh-hans/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [adapterremoval](https://www.automicvault.com/zh-hans/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [alevin-fry](https://www.automicvault.com/zh-hans/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [any2fasta](https://www.automicvault.com/zh-hans/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [augustus](https://www.automicvault.com/zh-hans/pkg/brew/augustus/) - Shares av.db curated category or tags: bioinformatics, cli, science.
- [fastk](https://www.automicvault.com/zh-hans/pkg/brew/fastk/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz.
- [tabixpp](https://www.automicvault.com/zh-hans/pkg/brew/tabixpp/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz.
- [vcflib](https://www.automicvault.com/zh-hans/pkg/brew/vcflib/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, science, xz.

## Combined YAML source

View the package source record on GitHub. [combined/bedtools.yml](https://github.com/automic-vault/db/blob/main/combined/bedtools.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