MAKER2 is a genome annotation and data management tool designed for second-generation genome projects. It addresses the challenges and opportunities presented by these projects, which often involve exotic organisms with limited or no pre-existing gene models. MAKER2 is a multi-threaded, parallelized application capable of processing large datasets. It can produce accurate annotations for novel genomes with limited or low-quality training data and uses mRNA-seq data to improve annotation quality. MAKER2 also evaluates the quality of annotations and identifies problematic annotations for manual review. The tool is the first specifically designed for second-generation genome projects, scaling to datasets of any size and requiring minimal training data. It can update and manage legacy genome annotation datasets, making it a comprehensive solution for modern genome annotation and management.MAKER2 is a genome annotation and data management tool designed for second-generation genome projects. It addresses the challenges and opportunities presented by these projects, which often involve exotic organisms with limited or no pre-existing gene models. MAKER2 is a multi-threaded, parallelized application capable of processing large datasets. It can produce accurate annotations for novel genomes with limited or low-quality training data and uses mRNA-seq data to improve annotation quality. MAKER2 also evaluates the quality of annotations and identifies problematic annotations for manual review. The tool is the first specifically designed for second-generation genome projects, scaling to datasets of any size and requiring minimal training data. It can update and manage legacy genome annotation datasets, making it a comprehensive solution for modern genome annotation and management.