# 使用 Homebrew, apt 安装 stringtie

查看 stringtie 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:stringtie
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install stringtie
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install stringtie
```

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

## 软件包事实

- **软件包键:** brew:stringtie
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/stringtie>
- **版本:** 3.0.3
- **来源摘要:** Transcript assembly and quantification for RNA-Seq
- **主页:** <https://github.com/gpertea/stringtie>
- **仓库:** <https://github.com/gpertea/stringtie>
- **许可证:** MIT
- **源码归档:** <https://github.com/gpertea/stringtie/archive/refs/tags/v3.0.3.tar.gz>
- **最后更新:** 2026-06-22T14:06:23-07:00
- **已生成:** 2026-08-04T22:13:35+00:00

## 可执行文件

- stringtie (cli)
- stringtie (别名)

## 依赖

- htslib

## 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: 2026-08-04
- 管理器版本: 3.0.3
- 管理器更新时间: 2026-06-22
- 本地数据: OK
- 上游仓库: https://github.com/gpertea/stringtie
- 检测到的最新版本: v3.0.3 (当前)
## 项目历史与用法

StringTie is a bioinformatics CLI for transcript assembly and quantification from RNA-Seq alignments, packaged for command-line genomics workflows rather than general developer tooling.

### 项目历史

The official Johns Hopkins CCB page describes StringTie as a fast assembler of RNA-Seq alignments into potential transcripts, using a network-flow algorithm and optional de novo assembly. The project README points users to the CCB site as the official documentation and source/binary package surface.

The CCB publication list anchors the project in the 2015 Nature Biotechnology paper introducing StringTie for improved transcriptome reconstruction from RNA-Seq reads. Later official release notes show the tool evolving through StringTie2 long-read support and StringTie3 features such as nascent-aware assembly.

### 采用历史

StringTie became part of the command-line genomics stack alongside aligners and downstream expression tools. The official manual describes input from sorted SAM/BAM/CRAM alignments and mentions common upstream aligners such as TopHat, HISAT2, STAR, and minimap2.

The supplied package-manager facts show Homebrew, Debian, and Ubuntu packaging, which matters for bioinformatics users who install complete pipelines on workstations, clusters, and reproducible analysis environments.

### 使用方式

Typical use is `stringtie [-o output.gtf] [options] read_alignments.bam`, producing GTF transcript structures and expression values. The manual documents reference-guided assembly, merge mode, expression-estimation mode, long-read mode, mixed short/long-read mode, and outputs for downstream differential-expression tools.

Package users care about the CLI because it composes cleanly with samtools, HISAT2, STAR, minimap2, Ballgown, DESeq2, edgeR, and workflow managers without requiring a graphical environment.

### 为什么软件包爱好者会关心

StringTie is a good example of a scientific binary that package managers keep useful by standardizing installation across macOS and Linux, especially when users need reproducible pipelines rather than hand-built lab software.

It also shows why package metadata matters in science: the same executable name, docs, license, and source repository need to be discoverable across brew, Debian-family systems, and workflow recipes.

### 时间线

- 2014-10-13: GitHub repository metadata records public repository creation.
- 2015: CCB publication list cites the Nature Biotechnology paper introducing StringTie.
- 2019: CCB publication list cites StringTie2 for transcriptome assembly from long-read RNA-seq alignments.
- 2021: Official release notes describe StringTie 2.2.0 support for mixed short- and long-read alignments and CRAM input.
- 2025: Official release notes describe StringTie 3.0.0 and nascent-aware assembly work.

### Related projects

- HISAT2, TopHat, STAR, minimap2, samtools, Ballgown, DESeq2, edgeR, gffcompare, and GFF utilities are adjacent tools named by the official docs or workflow context.

### 来源

- <https://ccb.jhu.edu/software/stringtie>
- <https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual>
- <https://github.com/gpertea/stringtie#readme>
- 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:** stringtie
- **Version Scheme:** 0
- **Revision:** 0
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable

## 其他软件包管理器记录

- Debian apt - stringtie - 2.2.1+ds-3+b1: normalized package name match | Debian stable package indexes: stringtie from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | assemble short RNAseq reads to transcripts | https://ccb.jhu.edu/software/stringtie/
- Ubuntu apt - stringtie - 2.2.1+ds-3build2: normalized package name match | Ubuntu 24.04 LTS package indexes: stringtie from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | assemble short RNAseq reads to transcripts | https://ccb.jhu.edu/software/stringtie/


## 相关链接

- [Source-control packages](https://pkg.so/zh-hans/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://pkg.so/zh-hans/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://pkg.so/zh-hans/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://pkg.so/zh-hans/scientific-computing-tools/) - Matched scientific computing metadata.
- [htslib](https://pkg.so/zh-hans/brew/htslib/) - Runtime dependency declared by Homebrew.
- [salmon](https://pkg.so/zh-hans/brew/salmon/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, quantification, rna-seq.
- [kallisto](https://pkg.so/zh-hans/brew/kallisto/) - Shares pkgdb curated category or tags: bioinformatics, cli, quantification, rna-seq, science.
- [rna-star](https://pkg.so/zh-hans/brew/rna-star/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, rna-seq, science.
- [samtools](https://pkg.so/zh-hans/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [blast](https://pkg.so/zh-hans/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [bedtools](https://pkg.so/zh-hans/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [minimap2](https://pkg.so/zh-hans/brew/minimap2/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [oarfish](https://pkg.so/zh-hans/brew/oarfish/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, quantification, rna, rna-seq.

## Combined YAML source

View the package source record on GitHub. [combined/stringtie.yml](https://github.com/mxcl/pkgdb/blob/main/combined/stringtie.yml)


## 来源

- pkg.so package database
- Geiger risk classifier
- package-page enrichment
- curated package history
- package version freshness
- pkgdb category and tag curation
- package relationship graph
- external package-manager database matches
- cross-ecosystem install command graph