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PRODID:-//Microsoft Corporation//Outlook MIMEDIR//EN
VERSION:2.0
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DTSTART:20151117T193000Z
DTEND:20151117T200000Z
LOCATION:18AB
DESCRIPTION;ENCODING=QUOTED-PRINTABLE:ABSTRACT: De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics.  This work presents the first high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. First, we significantly improve scalability of parallel k-mer analysis for complex repetitive genomes that exhibit skewed frequency distributions. Next, we optimize the traversal of the de Bruijn graph of k-mers by employing a novel communication-avoiding parallel algorithm in a variety of use-case scenarios. Finally, we parallelize the Meraculous scaffolding modules by leveraging the one-sided communication capabilities of the Unified Parallel C while effectively mitigating load imbalance. Large-scale results on a Cray XC30 using grand-challenge genomes, demonstrate efficient performance and scalability on thousands of cores. Overall, our pipeline accelerates Meraculous performance by orders of magnitude, creating unprecedented capability for extreme-scale genomic analysis.
SUMMARY:HipMer: An Extreme-Scale De Novo Genome Assembler
PRIORITY:3
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