GffRead and GffCompare are open-source programs designed to manipulate and compare genomic feature files in GTF and GFF formats. GffRead can convert, sort, filter, transform, or cluster genomic features, while GffCompare can compare and merge different gene annotations. Both tools are implemented in C++ for Linux and OS X and are released under an MIT license. They are widely used in bioinformatics pipelines for genome annotation, novel gene discovery, and transcriptome analysis. The article provides detailed descriptions of their functionalities, including their ability to handle large datasets and their applications in various bioinformatics workflows. The tools are available on GitHub and can be used as command-line programs, offering a user-friendly interface for efficient genomic data processing.GffRead and GffCompare are open-source programs designed to manipulate and compare genomic feature files in GTF and GFF formats. GffRead can convert, sort, filter, transform, or cluster genomic features, while GffCompare can compare and merge different gene annotations. Both tools are implemented in C++ for Linux and OS X and are released under an MIT license. They are widely used in bioinformatics pipelines for genome annotation, novel gene discovery, and transcriptome analysis. The article provides detailed descriptions of their functionalities, including their ability to handle large datasets and their applications in various bioinformatics workflows. The tools are available on GitHub and can be used as command-line programs, offering a user-friendly interface for efficient genomic data processing.