macOS
Homebrewverifiziert · 100%
brew install gffreadlocal Homebrew formula metadata
brew
gffread mit Homebrew, apt installieren
Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für gffread in AI-Agent-Workflows.
Installation
Weitere Installationsbefehle
Linux
Debian aptverifiziert · 92%
sudo apt install gffreadDebian stable package indexes · gffread · Quelle: deb.debian.org
Überblick
Paketzusammenfassung
GFF/GTF format conversions, region filtering, FASTA sequence extraction
Projektlinks
Befehle und Aliase
- gffread
Verlauf
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
Sicherheitslage
Risikostufe: grün
narrow executable package without higher-risk signals.
Risikoklassifikator
grün Risiko · niedrig Konfidenz · appliance
Warum
- narrow executable package without higher-risk signals
Signale
- metadata:no-higher-risk-signals
Installationsverhalten
- In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
- Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
Empfohlene Prüfung
Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.
Executables
Installierte Executables
| Befehl | Art | Sichtbarkeit | Hinweis |
|---|---|---|---|
gffread | cli | globales Executable |
Aktualität
Version und Aktualität
Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.
Seite generiert2026-07-08
Manager-Version0.12.9
Manager aktualisiert2026-04-10
lokale DatenOK
Upstreamnot checked
neueste erkannte Versionnicht erkannt
https://github.com/gpertea/gffread
- InfoNo cached GitHub release or tag data was available.https://github.com/gpertea/gffreadnone Konfidenz
Installationsmetadaten
Paketmetadaten
| Paketschlüssel | brew:gffread |
|---|---|
| Version | 0.12.9 |
| Paketmanager | Homebrew |
| Paketmanager-Seite | https://formulae.brew.sh/formula/gffread |
| 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 |
| Pulse | updated |
| Bottle | verfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | nicht definiert |
| Dienst | keiner deklariert |
Registry-Fakten
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 |
|
Source-Datenbank-Treffer
Andere Paketmanager-Einträge
Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.
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 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: 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 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Gffread
Quellspur
Aus Repository-Daten generiert
Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.
Combined YAML source
View the package source record on GitHub.
Verwendete Quellen
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment