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DTSTAMP:20181221T160743Z
LOCATION:C2/3/4 Ballroom
DTSTART;TZID=America/Chicago:20181114T083000
DTEND;TZID=America/Chicago:20181114T170000
UID:submissions.supercomputing.org_SC18_sess342_drs108@linklings.com
SUMMARY:Parallel and Scalable Combinatorial String and Graph Algorithms on
  Distributed Memory Systems
DESCRIPTION:Doctoral Showcase\nWorkshop Reg Pass, Tutorial Reg Pass, Tech 
 Program Reg Pass, Exhibits Reg Pass, Exhibits - Exhibit Hall Only Reg Pass
 \n\nParallel and Scalable Combinatorial String and Graph Algorithms on Dis
 tributed Memory Systems\n\nFlick, Aluru\n\nMethods for processing and anal
 yzing DNA and genomic data are built upon combinatorial graph and string a
 lgorithms. The advent of high-throughput DNA sequencing is enabling the ge
 neration of billions of reads per experiment. Classical and sequential alg
 orithms can no longer deal with these growing data sizes, which for the la
 st 10 years have greatly out-paced advances in processor speeds. To proces
 s and analyze state-of-the-art genomic data sets require the design of sca
 lable and efficient parallel algorithms and the use of large computing clu
 sters. Here, we present our distributed-memory parallel algorithms for ind
 exing large genomic datasets, including algorithms for construction of suf
 fix- and LCP arrays, solving the All-Nearest-Smaller-Values problem and it
 s application to the construction of suffix trees. Our parallel algorithms
  exhibit superior runtime complexity and practical performance compared to
  the state-of-the-art. Furthermore, we present distributed-memory algorith
 ms for clustering de-Bruijn graphs and its application to solving a grand 
 challenge metagenomic dataset.
URL:https://sc18.supercomputing.org/presentation/?id=drs108&sess=sess342
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