Abstract
MOTIVATION: The volume of multi-omics data for diverse species is growing at an unprecedented rate, with new genome assemblies, related annotations, and high-throughput sequencing resources being submitted daily to various genomic data repositories. In response to this data influx, both existing and new databases are establishing optimized hierarchical structures to manage the vast amount of information. However, the lack of accessible command-line tools, combined with the functional limitations and unintuitive design of existing options, presents significant challenges for researchers. This gap underscores a critical need for a tool that enables streamlined retrieval and integration of omics data across these diverse repositories. RESULTS: We have developed Gencube, a command-line tool that enables centralized retrieval and integration of a comprehensive set of six different data types-genome assemblies, gene sets, annotations, sequences, comparative genomic data, and NGS-based omics resources-from various leading databases. AVAILABILITY AND IMPLEMENTATION: Gencube is a free and open-source tool, with its code available on GitHub: https://github.com/snu-cdrc/gencube and also archived on Zenodo: https://doi.org/10.5281/zenodo.14607649.