# gffread を Homebrew, apt でインストール

gffread のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

## インストール

```sh
sudo av install brew:gffread
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install gffread
```

  証拠: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install gffread
```

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

## パッケージ情報

- **パッケージキー:** brew:gffread
- **パッケージマネージャ:** Homebrew
- **パッケージマネージャページ:** <https://formulae.brew.sh/formula/gffread>
- **バージョン:** 0.12.9
- **ソース概要:** GFF/GTF format conversions, region filtering, FASTA sequence extraction
- **ホームページ:** <https://github.com/gpertea/gffread>
- **リポジトリ:** <https://github.com/gpertea/gffread>
- **上流ドキュメント:** <http://ccb.jhu.edu/software/stringtie/gff.shtml>
- **ライセンス:** MIT
- **ソースアーカイブ:** <https://github.com/gpertea/gffread/releases/download/v0.12.9/gffread-0.12.9.tar.gz>
- **最終更新:** 2026-04-10T21:12:05Z
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- gffread (cli)
- gffread (エイリアス)

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-07-08
- マネージャ版: 0.12.9
- マネージャ更新日: 2026-04-10
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/gpertea/gffread
- 情報: No cached GitHub release or tag data was available.
## プロジェクトの歴史と使われ方

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.

### プロジェクトの歴史

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.

### 採用の歴史

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.

### 使われ方

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.

### パッケージ好きにとっての重要性

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.

### タイムライン

- 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.

### ソース

- <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/>


## セキュリティノート

narrow executable package without higher-risk signals.

- **Geiger リスク:** グリーン / 低
- narrow executable package without higher-risk signals

## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** gffread
- **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

## 他のパッケージマネージャ記録

- 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


## 関連リンク

- [Source-control packages](https://www.automicvault.com/ja/pkg/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Text processing packages](https://www.automicvault.com/ja/pkg/text-processing-tools/) - Matched text, document, or structured-data processing metadata.
- [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [abricate](https://www.automicvault.com/ja/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [minigraph](https://www.automicvault.com/ja/pkg/brew/minigraph/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [stringtie](https://www.automicvault.com/ja/pkg/brew/stringtie/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [tabixpp](https://www.automicvault.com/ja/pkg/brew/tabixpp/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [vcfanno](https://www.automicvault.com/ja/pkg/brew/vcfanno/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [vcflib](https://www.automicvault.com/ja/pkg/brew/vcflib/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [vcftools](https://www.automicvault.com/ja/pkg/brew/vcftools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science.
- [any2fasta](https://www.automicvault.com/ja/pkg/brew/any2fasta/) - Shares av.db curated category or tags: bioinformatics, cli, fasta, science.

## Combined YAML source

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


## ソース

- 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