AGAVE: Automated Genomics Application for Variant Exploration

Abstract

The Johns Hopkins University Applied Physics Laboratory (APL) is actively developing new capabilities for genomic surveillance of viruses. APL genomicists analyze, process, and visualize viral genomic data for several sponsor organizations that require those data to inform clinical, research, and public policy decisions. Many of the final products from these processes are delivered to sponsors as static reports or slide presentations, but it can be arduous to review or extract pertinent information from these documents. APL genomicists wanted to improve their sponsors’ ability to analyze their data and rapidly identify genomic samples or sequences they find important for decision-making. With this goal in mind, a group of APL software engineers developed the Automated Genomics Application for Variant Exploration (AGAVE). AGAVE is an interactive, intuitive web-based tool where researchers can explore and analyze genomic data, draw new connections between data points, and understand the significance behind genomic variants quickly. Researchers can view their sequence data, choose a reference genome with which to compare the data, visualize the 3-D structure of proteins that would be created from particular segments of DNA, and export those visualizations as easily shared image files. AGAVE is still under development and currently supports only influenza genomes, but as it matures and its user base grows, it will expand beyond influenza to include other viruses such as SARS-CoV-2 and even bacterial genomes.