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DTSTART;TZID=America/Chicago:20181113T111500
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UID:submissions.supercomputing.org_SC18_sess277_drs102@linklings.com
SUMMARY:Scalable Methods for Genome Assembly
DESCRIPTION:Doctoral Showcase\nComputational Biology, Exascale, GPUs, Grap
 h Algorithms, Linear Algebra, Machine Learning, Sparse Computation, Worksh
 op Reg Pass, Tutorial Reg Pass, Tech Program Reg Pass, Exhibits Reg Pass, 
 Exhibits - Exhibit Hall Only Reg Pass, Doctoral Showcase\n\nScalable Metho
 ds for Genome Assembly\n\nGhosh, Kalyanaraman\n\nGenome assembly is a fund
 amental problem in the field of bioinformatics wherein the goal lies in th
 e reconstruction of an unknown genome from short DNA fragments obtained fr
 om it. With the advent of high-throughput sequencing technologies, billion
 s of reads can be generated in a few hours. My reseach deals with addressi
 ng the challenges of conducting genome assembly at scale and developing ne
 w methods for conducting extreme-scale genome assembly suited for microbia
 l genomes, and complex eukaryotic genomes. Our approach to the problem is 
 two-fold, wherein we target fast and space-efficient assemblies of moderat
 e sized genomes on a single node with our shared-memory based implementati
 on (FastEtch). Secondly we aim to tackle the assembly of very large genome
 s with our distributed-memory based approach (PaKman), in an attempt to mi
 nimize the turnaround time such that it could potentially pave the way to 
 conducting the assembly process in real-time.
URL:https://sc18.supercomputing.org/presentation/?id=drs102&sess=sess277
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