# gffread mit Homebrew, apt installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für gffread in AI-Agent-Workflows.

## Installation

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

Weitere Installationsbefehle:

### macOS

- Homebrew (100%):

```sh
brew install gffread
```

  Evidenz: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install gffread
```

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

## Paketfakten

- **Paketschlüssel:** brew:gffread
- **Paketmanager:** Homebrew
- **Paketmanager-Seite:** <https://formulae.brew.sh/formula/gffread>
- **Version:** 0.12.9
- **Quellzusammenfassung:** GFF/GTF format conversions, region filtering, FASTA sequence extraction
- **Homepage:** <https://github.com/gpertea/gffread>
- **Repository:** <https://github.com/gpertea/gffread>
- **Upstream-Dokumentation:** <http://ccb.jhu.edu/software/stringtie/gff.shtml>
- **Lizenz:** MIT
- **Quellarchiv:** <https://github.com/gpertea/gffread/releases/download/v0.12.9/gffread-0.12.9.tar.gz>
- **Zuletzt aktualisiert:** 2026-04-10T21:12:05Z
- **Generiert:** 2026-07-08T18:08:21+00:00

## Executables

- gffread (cli)
- gffread (Alias)

## Installationsverhalten

- Post-install-Hook: nicht definiert
- Bottle: verfügbar auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## Version und Aktualität

- Seite generiert: 2026-07-08
- Manager-Version: 0.12.9
- Manager aktualisiert: 2026-04-10
- lokale Daten: OK
- Upstream-Repository: https://github.com/gpertea/gffread
- Info: No cached GitHub release or tag data was available.
## Projektgeschichte und Nutzung

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.

### Projektgeschichte

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.

### Adoptionsgeschichte

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.

### Wie es verwendet wird

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.

### Warum Paket-Nerds sich dafür interessieren

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.

### Zeitleiste

- 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.

### Quellen

- <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/>


## Sicherheitshinweise

narrow executable package without higher-risk signals.

- **Geiger-Risiko:** grün / niedrig
- narrow executable package without higher-risk signals

## Details aus der Quelldatenbank

- **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

## Andere Paketmanager-Einträge

- 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


## Verwandte Links

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


## Quellen

- 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