# Install gffread with Homebrew, apt

GFF/GTF format conversions, region filtering, FASTA sequence extraction. Version 0.12.9 via Homebrew; verified from local package data. Also installable with debian: sudo apt install gffread.

## Install

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

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install gffread
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install gffread
```

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

## Package facts

- **Package key:** brew:gffread
- **Package manager:** Homebrew
- **Version:** 0.12.9
- **Source summary:** GFF/GTF format conversions, region filtering, FASTA sequence extraction
- **Homepage:** <https://github.com/gpertea/gffread>
- **Repository:** <https://github.com/gpertea/gffread>
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- gffread (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 0.12.9
## 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

- <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/>


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Other Package-Manager Records

- 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


## Combined YAML source

View the package source record on GitHub. [combined/gffread.yml](https://github.com/mxcl/pkgdb/blob/main/combined/gffread.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph