Understanding biodiversity through a global platform for assembly and analysis of large genomes

Nationally, a significant investment is made each year in genome sequencing. This investment is critical for expanding our understanding of biology, enhancing and optimizing agricultural output, as well as improving human health. However, sequencing by itself does not translate into these advances. This project aims at developing critical infrastructure components necessary for interpretation of genomic data. As a result of this work, cutting edge tools, workflows, and tutorials will become available to a much wider audience of biology researchers. Training is a dedicated aim, and tools will be made usable, as well as comprehensible for non-specialist users. Importantly, the project will also leverage public NSF-funded cyberinfrastructure to run these tools at scale. This project is one of the first in which high-quality genome sequence assembly workflows will become available for immediate use to a wide audience of biologists. Combined with comprehensive documentation and tutorials, the infrastructure deployed will have a profound effect on the quality and number of genome assemblies, translating into downstream discoveries. It will streamline access to information important for basic research, including for biodiversity research, molecular genetics, evolutionary analyses, and biogeography, helping to ensure planetary resilience. Making assembly and alignment methods widely accessible will contribute significantly to the bioeconomy, ensuring that national investments on sequencing projects provide return in the form of new knowledge important for basic and applied research. Relying on public computational infrastructure will open these tools and workflows to immediate use by all researchers, whether or not they have access to computing and domain expertise, fostering equitable genomics. Development of a dedicated toolkit for manipulation and analysis of whole-genome alignment will make newly created as well as already existing alignments much more useful for downstream analyses; any researcher will be able to study the evolution of their gene/genes of interest. Finally, the comprehensive portfolio of interactive training materials we will develop will be the first training effort in comparative genomics with a global reach.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.