macOS
Homebrew已验证 · 100%
brew install gffreadlocal Homebrew formula metadata
安装
其他安装命令
Linux
Debian apt已验证 · 92%
sudo apt install gffreadDebian stable package indexes · gffread · 来源: deb.debian.org
概览
软件包摘要
GFF/GTF format conversions, region filtering, FASTA sequence extraction
项目链接
命令和别名
- gffread
历史
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
安全态势
风险级别：绿色
narrow executable package without higher-risk signals.
风险分类器
绿色 风险 · 低 置信度 · appliance
原因
- narrow executable package without higher-risk signals
信号
- metadata:no-higher-risk-signals
安装行为
- 未记录 Homebrew bottle 元数据。
建议审查
在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。
可执行文件
已安装的可执行文件
| 命令 | 类型 | 暴露范围 | 备注 |
|---|---|---|---|
gffread | 可执行文件 | 已索引可执行文件 | 从本地可执行文件索引发现。 |
新鲜度
版本和新鲜度
这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。
页面生成时间2026-08-03
管理器版本0.12.9
管理器更新时间
本地数据未知
上游不可用
检测到的最新版本未检测到
- OK没有生成新鲜度警告。
安装元数据
软件包元数据
| 软件包键 | brew:gffread |
|---|---|
| 版本 | 0.12.9 |
| 软件包管理器 | Homebrew |
| 主页 | https://github.com/gpertea/gffread |
| 仓库 | https://github.com/gpertea/gffread |
| Bottle | 未记录 |
| 服务 | 未声明 |
源数据库匹配
其他软件包管理器记录
匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。
Debian apt95%
gffread 0.12.7-8
GFF/GTF format conversions, region filtering, FASTA sequence extraction
https://ccb.jhu.edu/software/stringtie/gff.shtml
sudo apt install gffread- Section: science
- Architecture: amd64
- 3 依赖
- normalized package name match
- 匹配方式：Gffread
Ubuntu apt95%
gffread 0.12.7-4build1
GFF/GTF format conversions, region filtering, FASTA sequence extraction
https://ccb.jhu.edu/software/stringtie/gff.shtml
sudo apt install gffread- Section: universe/science
- Architecture: amd64
- 3 依赖
- normalized package name match
- 匹配方式：Gffread
来源线索
由仓库数据生成
此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。
Combined YAML source
View the package source record on GitHub.
使用的来源
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation