Bioinformatics Analysis Tools for Studying Microbiomes at the DOE Joint Genome Institute

The DOE Joint Genome Institute has developed and maintains a number of computational resources and databases to help biologists perform -omics-based scientific research. In this review, we describe two of its widely used microbiome data management and analysis resources: the Genome OnLine Database (GOLD) and the Integrated Microbial Genomes (IMG). GOLD is a sequencing project and associated metadata management system. It provides a catalog of genome and metagenome projects with well-curated associated metadata which are critical for sequence data interpretation. IMG is an omics data management system enabling the comparative analysis of microbial genomes, metagenomes, and metatranscriptomics and their associated genes and functions. IMG contains close to 200,000 datasets and provides advanced search and comparative analysis tools. GOLD’s metadata are integrated into IMG to provide a better understanding of the environments and properties of each dataset. In addition to all the public data integrated, both systems support private user data submission and integration to support annotation and comparative analysis with all other data integrated into the systems. There are currently over 25,000 registered users from more than 110 countries, and the systems are also used for educational purposes across various universities around the world.