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brew / rank 6535

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 commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install gffread

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install gffread

Debian stable package indexes · gffread · source: deb.debian.org

overview

Package summary

GFF/GTF format conversions, region filtering, FASTA sequence extraction

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.

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 bottle metadata was recorded.

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

CommandKindExposureNote
gffreadexecutableindexed executableDiscovered from the local executable index.

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 generated2026-08-03
manager version0.12.9
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:gffread
Version0.12.9
Package managerHomebrew
Homepagehttps://github.com/gpertea/gffread
Repositoryhttps://github.com/gpertea/gffread
Bottlenot recorded
Servicenone declared

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
Debian stable package indexes · deb.debian.org · Debian stable package indexes: gffread from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: gffread from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

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.

Used sources

  • 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