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  1. Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performancemore »genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.« less
  2. Abstract 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 community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilersmore »markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.« less
    Free, publicly-accessible full text available April 1, 2023