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DOE OSTI · 2459350

Exabiome: Advancing Microbial Science through Exascale Computing

Hofmeyr, Steven·Buluç, Aydin·Riley, Robert·Egan, Rob·Selvitopi, Oguz·Oliker, Leonid·Yelick, Katherine·Shakya, Migun·Youtsey, Brett·Azad, Ariful
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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.

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59 BASIC BIOLOGICAL SCIENCES97 MATHEMATICS AND COMPUTINGAssemblyBioinformatics Analysis PipelineBiomanufacturingCandidate PhylaComparative AnalysisComponent Of The ProjectDark MatterExascale ComputingHash FunctionHigh-performance ComputingHuman MicrobiomeHuman Microbiome ProjectJoint Genome InstituteMetagenome-assembled GenomesMetagenomic AnalysisMetagenomic AssemblyMetagenomic SamplesMetagenomicsMicrobial CommunityMicrobiologyMicrobiome SpeciesMicroorganismsNaked EyePairwise DistancesPercentage Of SpeciesProtein FamilyProtein PairsProtein Sequence SimilarityProtein SequencesProtein engineeringRedoxScientific FindingsScientific ImpactSequential analysisSparse MatrixTara OceansUnderstanding Of Microbiome

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Hofmeyr, Steven, Buluç, Aydin, Riley, Robert, Egan, Rob, Selvitopi, Oguz, Oliker, Leonid, Yelick, Katherine, Shakya, Migun, Youtsey, Brett, Azad, Ariful. 2024-05-22. Exabiome: Advancing Microbial Science through Exascale Computing. https://doi.org/10.1109/mcse.2024.3402546

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