GffRead and GffCompare are open-source tools for manipulating GTF and GFF files, widely used in bioinformatics for genome annotation and transcript analysis. GffRead converts, sorts, filters, and clusters genomic features, while GffCompare compares and merges transcript annotations. Both tools are implemented in C++ and available under an MIT license. They support GFF3 and GTF formats, as well as BED and FASTA conversions. GffRead can extract transcript sequences and annotate features, while GffCompare assesses transcript accuracy against reference annotations and tracks transcript structures across samples. The tools are efficient, user-friendly, and widely adopted in genome analysis pipelines. They handle large datasets and provide detailed output for transcript classification, including super-locus identification and structural equivalence. The software is compatible with Linux and macOS, with precompiled binaries available. The article describes the tools' functions, implementation, use cases, and peer review feedback, highlighting their utility in transcriptome analysis and gene annotation.GffRead and GffCompare are open-source tools for manipulating GTF and GFF files, widely used in bioinformatics for genome annotation and transcript analysis. GffRead converts, sorts, filters, and clusters genomic features, while GffCompare compares and merges transcript annotations. Both tools are implemented in C++ and available under an MIT license. They support GFF3 and GTF formats, as well as BED and FASTA conversions. GffRead can extract transcript sequences and annotate features, while GffCompare assesses transcript accuracy against reference annotations and tracks transcript structures across samples. The tools are efficient, user-friendly, and widely adopted in genome analysis pipelines. They handle large datasets and provide detailed output for transcript classification, including super-locus identification and structural equivalence. The software is compatible with Linux and macOS, with precompiled binaries available. The article describes the tools' functions, implementation, use cases, and peer review feedback, highlighting their utility in transcriptome analysis and gene annotation.