macOS
Homebrewverified · 100%
brew install gffreadlocal Homebrew formula metadata
brew
Install gffread with Homebrew, apt
GFF/GTF format conversions, region filtering, FASTA sequence extraction. Version 0.12.9 via Homebrew; verified 2026-04-10.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install gffreadDebian stable package indexes · gffread · source: deb.debian.org
overview
Package summary
GFF/GTF format conversions, region filtering, FASTA sequence extraction
Project links
Commands and aliases
- gffread
history
Project history and usage
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.
Project history
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.
Adoption history
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.
How it is used
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.
Why package nerds care
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.
Timeline
- 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.
Sources
security posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew post-install hook is recorded in formula metadata.
- Homebrew bottle metadata is available for 6 platform targets.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
gffread | cli | global executable |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-07-08
manager version0.12.9
manager updated2026-04-10
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/gpertea/gffread
- infoNo cached GitHub release or tag data was available.https://github.com/gpertea/gffreadnone confidence
install metadata
Package metadata
| Package key | brew:gffread |
|---|---|
| Version | 0.12.9 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/gffread |
| Homepage | https://github.com/gpertea/gffread |
| Repository | https://github.com/gpertea/gffread |
| Upstream docs | http://ccb.jhu.edu/software/stringtie/gff.shtml |
| License | MIT |
| Source archive | https://github.com/gpertea/gffread/releases/download/v0.12.9/gffread-0.12.9.tar.gz |
| Last updated | 2026-04-10T21:12:05Z |
| Pulse | updated |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| 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 database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
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 dependencies
- normalized package name match
- Matched by: 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 dependencies
- normalized package name match
- Matched by: Gffread
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- 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