Exabiome: Advancing Microbial Science through Exascale Computing

Abstract

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of "dark matter" proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location. Microbiomes are profoundly important in many different areas, such as human health, farming, the environment and bio-manufacturing. Microbiomes are comprised of communities of thousands of microbial species, organisms too small to be seen by the naked eye, such as bacteria, protozoa, fungi and viruses. Much of a deeper understanding of these communities comes from an analysis of the genetics of the various species, a task that is made difficult by the fact that less than one percent of species in a microbiome are individually culturable in a laboratory. This led to metagenomics, where samples that include most of the genomes in the community are sequenced and analyzed to identify new species, characterize taxonomic diversity, provide functional annotation, and generally enhance understanding of microbiomes.The collection of sequencing data is increasing XXXX-XXX © IEEE Digital Object Identifier 10.1109/XXX.0000.0000000