Comprehensive structural characterization of protein-coding gene repertoires is a crucial step to identify differences and commonalities in comparative genomics contexts. This requires a descriptive set of standardized parameters as well as summary statistics of, e.g., gene lengths and exon counts. We developed the tool COGNATE to gather this data from a given structural annotation file in combination with the corresponding genome assembly with a single simple command line call. COGNATE relies on clearly stated parameter definitions and thus serves to enhance dataset comparability. Here, it is shown how the tool can be used; special attention is given to input formatting.