Gencube: Efficient retrieval, download, and unification of genomic data from leading biodiversity databases

Motivation With the daily submission of numerous new genome assemblies, associated annotations, and experimental sequencing data to genome archives for various species, the volume of genomic data is growing at an unprecedented rate. Major genomic databases are establishing new hierarchical structures to manage this data influx. However, there is a significant need for tools that can efficiently access, download, and integrate genomic data from these diverse repositories, making it challenging for researchers to keep pace. Results We have developed Gencube , a command-line tool with two primary functions. First, it facilitates the utility of genome assemblies, related annotations, gene set sequences, and cross-species data from various leading biodiversity databases. Second, it helps researchers intuitively explore experimental sequencing data that meets their needs and consolidates the metadata of the retrieved outputs. Availability and implementation Gencube is a free and open-source tool, with its code available on GitHub: https://github.com/snu-cdrc/gencube .