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DTSTAMP:20260522T150117Z
LOCATION:C140/142
DTSTART;TZID=America/Chicago:20181113T133000
DTEND;TZID=America/Chicago:20181113T140000
UID:submissions.supercomputing.org_SC18_sess206_pap410@linklings.com
SUMMARY:Extreme Scale De Novo Metagenome Assembly
DESCRIPTION:Evangelos Georganas (Intel Corporation) and Rob Egan, Steven H
 ofmeyr, Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluc, Leonid Oli
 ker, and Katherine Yelick (Lawrence Berkeley National Laboratory)\n\nMetag
 enome assembly is the process of transforming a set of short, overlapping,
  and potentially erroneous DNA segments from environmental samples into th
 e accurate representation of the underlying microbiomes's genomes. State-o
 f-the-art tools require large shared memory machines and cannot handle con
 temporary metagenome datasets that exceed terabytes in size. In this paper
 , we introduce the metaHipMer pipeline, a high-quality and high-performanc
 e metagenome assembler that employs an iterative de Bruijn graph approach.
  MetaHipMer leverages a specialized scaffolding algorithm that produces lo
 ng scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMe
 r is end-to-end parallelized using the Unified Parallel C language and the
 refore can run seamlessly on shared and distributed-memory systems. Experi
 mental results show that metaHipMer matches or outperforms the state-of-th
 e-art tools in terms of accuracy. Moreover, metaHipMer scales efficiently 
 to large concurrencies and is able to assemble previously intractable gran
 d challenge metagenomes.\n\nTag: Algorithms, Applications, Computational B
 iology, Scientific Computing\n\nRegistration Category: Tech Program Reg Pa
 ss\n\nFinalist: BP Finalist\n\nSession Chair: Allison H. Baker (National C
 enter for Atmospheric Research (NCAR))\n\n
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