gffread ☆

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

Type: Formula | Tracked Since: Dec 28, 2025

Links: Homepage | formulae.brew.sh

Category: Other

Tags: bioinformatics gff gtf genomics sequence-analysis

Install: brew install gffread

About:
Gffread is a versatile command-line utility for validating, filtering, and converting GFF and GTF annotation files. It can extract genomic sequences from a FASTA file based on GFF coordinates, generate cDNA sequences, and produce standard-compliant output formats. This tool is essential for preparing and refining annotation data for downstream bioinformatics analysis.

Key Features:

Converts between GFF and GTF formats
Filters annotations by attribute, region, or class code
Extracts and translates cDNA or protein sequences from genomic FASTA
Validates and sorts annotation records for consistency

Use Cases:

Generating cDNA sequences from a genome and annotation set
Standardizing annotation formats for compatibility with different tools
Selecting specific gene or transcript subsets from large annotation files

Alternatives:

agat – Another comprehensive toolkit for GFF/GTF manipulation, often used for more complex annotation processing.
bedtools – A general-purpose toolkit for genomic arithmetic, which can perform some overlapping tasks like sequence extraction.

Version History

Detected	Version	Rev	Change	Commit
Sep 11, 2025 12:36pm		0	VERSION_BUMP	51b0195b
Sep 13, 2024 8:45am		0	VERSION_BUMP	970940ea