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Article
Open AccessCritical Assessment of Metagenome Interpretation: the second round of challenges
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the co...
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Chapter and Conference Paper
Towards Flexible and Compiler-Friendly Layer Fusion for CNNs on Multicore CPUs
In deep learning pipelines, we demonstrate the performance benefits and tradeoffs of combining two convolution layers into a single layer on multicore CPUs. We analyze when and why fusion may result in runtime...
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Article
Open AccessTerabase-scale metagenome coassembly with MetaHipMer
Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) an...
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Chapter and Conference Paper
A New Parallel Research Kernel to Expand Research on Dynamic Load-Balancing Capabilities
The Parallel Research Kernels (PRK) are a tool to study parallel architectures and runtime systems from an application perspective. They provide paper and pencil specifications and reference implementations of...
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Chapter and Conference Paper
Performance Characterization of De Novo Genome Assembly on Leading Parallel Systems
De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and ir...
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Article
Open AccessA whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic map**, we derive, de novo, a...
