# 使用 Homebrew, apt 安装 gffread

查看 gffread 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:gffread
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install gffread
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install gffread
```

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

## 软件包事实

- **软件包键:** brew:gffread
- **软件包管理器:** Homebrew
- **版本:** 0.12.9
- **来源摘要:** GFF/GTF format conversions, region filtering, FASTA sequence extraction
- **主页:** <https://github.com/gpertea/gffread>
- **仓库:** <https://github.com/gpertea/gffread>
- **已生成:** 2026-08-03T19:37:03+00:00

## 可执行文件

- gffread (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: 0.12.9
## 项目历史与用法

GffRead is a C++ command-line utility for reading, validating, converting, filtering, and extracting sequence data from GFF and GTF genome annotation files. Its history is closely linked to the StringTie/Cufflinks transcript-assembly ecosystem and to the practical need for robust interchange between GTF2 and GFF3.

### 项目历史

The Johns Hopkins Center for Computational Biology documents GffRead as part of its GFF utilities page, alongside GffCompare. The repository describes it as a GFF/GTF utility and points users to the 2020 F1000Research paper by Geo Pertea and Mihaela Pertea for usage examples and citation.

### 采用历史

GTF and GFF are common bioinformatics exchange formats for genes, transcripts, exons, and coding regions. GffRead gained significance because it uses parser code shared with Cufflinks, StringTie, and GffCompare, allowing researchers to test whether an annotation file will be interpreted by that tool family.

### 使用方式

Practitioners run GffRead to clean and inspect annotation files, convert GTF2 to GFF3 or GFF3 to GTF2, expose parser warnings, discard non-essential attributes, and extract transcript FASTA sequences from a genome FASTA plus annotation file. FASTA index files generated by samtools can speed sequence extraction.

### 为什么软件包爱好者会关心

GffRead is the sort of bioinformatics CLI that package managers keep close to workflow engines: small enough to install as a standalone binary, but important enough to sit inside larger RNA-seq and genome-annotation pipelines.

### 时间线

- 2020: The GFF Utilities paper described GffRead and GffCompare in F1000Research.
- 2020: Johns Hopkins publication metadata listed the software as open source under the MIT license.
- 2026: The project repository and Bioconda metadata listed v0.12.9 packages.

### Related projects

- GffRead is related to GffCompare, StringTie, Cufflinks, samtools, GTF2, and GFF3 tooling.

### 来源

- <http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread>
- <https://anaconda.org/bioconda/gffread>
- <https://github.com/gpertea/gffread>
- <https://pure.johnshopkins.edu/en/publications/gff-utilities-gffread-and-gffcompare/>


## 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 - gffread - 0.12.7-8: normalized package name match | Debian stable package indexes: gffread from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | GFF/GTF format conversions, region filtering, FASTA sequence extraction | https://ccb.jhu.edu/software/stringtie/gff.shtml
- Ubuntu apt - gffread - 0.12.7-4build1: normalized package name match | Ubuntu 24.04 LTS package indexes: gffread from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | GFF/GTF format conversions, region filtering, FASTA sequence extraction | https://ccb.jhu.edu/software/stringtie/gff.shtml


## Combined YAML source

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