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DTSTAMP:20181221T160729Z
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:Paper\nAlgorithms, Applications, Computational Biology, Scient
 ific Computing, Tech Program Reg Pass, BP Finalist\n\nExtreme Scale De Nov
 o Metagenome Assembly\n\nGeorganas, Egan, Hofmeyr, Goltsman, Arndt...\n\nM
 etagenome assembly is the process of transforming a set of short, overlapp
 ing, and potentially erroneous DNA segments from environmental samples int
 o the accurate representation of the underlying microbiomes's genomes. Sta
 te-of-the-art tools require large shared memory machines and cannot handle
  contemporary metagenome datasets that exceed terabytes in size. In this p
 aper, we introduce the metaHipMer pipeline, a high-quality and high-perfor
 mance metagenome assembler that employs an iterative de Bruijn graph appro
 ach. MetaHipMer leverages a specialized scaffolding algorithm that produce
 s long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaH
 ipMer is end-to-end parallelized using the Unified Parallel C language and
  therefore can run seamlessly on shared and distributed-memory systems. Ex
 perimental results show that metaHipMer matches or outperforms the state-o
 f-the-art tools in terms of accuracy. Moreover, metaHipMer scales efficien
 tly to large concurrencies and is able to assemble previously intractable 
 grand challenge metagenomes.
URL:https://sc18.supercomputing.org/presentation/?id=pap410&sess=sess206
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