SC is the International Conference for
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Storage and Analysis

SCHEDULE: NOV 12-18, 2011

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Fast GPU Read Alignment with Burrows Wheeler Transform Based Index

SESSION: Research Poster Reception

EVENT TYPE: ACM Student Research Competition Poster, Poster, Electronic Poster

TIME: 5:15PM - 7:00PM


AUTHOR(S):Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka

ROOM:WSCC North Galleria 2nd/3rd Floors

We addresses the problem of performing faster read alignment on GPU devices. This task is extremely computationally intensive as constant progress in sequencing technology leads to everincreasing amounts of sequence data. One of possible solutions for this problem is using the extreme parallel capacities of modern GPU devices. We found memory limitations to be main performance issue in previous solutions. Attempts have been made to decrease memory consumption of the matching algorithm, and we suggest to make another step in this direction by building a much smaller index using Burrows-Wheeler Transform. At the same time we use suffix array on host to have constant size output from each kernel and exploit different computational characteristics of both GPU and CPU. We reduced index size 12 times and achieved 3-4 time performance improvement.

Chair/Author Details:

Bernd Mohr (Chair) - Juelich Supercomputing Centre

Aleksandr Drozd - Tokyo Institute of Technology

Naoya Maruyama - Tokyo Institute of Technology

Satoshi Matsuoka - Tokyo Institute of Technology

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