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Paper Abstract and Keywords
Presentation 2013-05-20 15:50
FPGA Acceleration of Short Read Mapping
Yoko Sogabe, Tsutomu Maruyama (Univ. of Tsukuba) RECONF2013-4
Abstract (in Japanese) (See Japanese page) 
(in English) The rapid development of Next Generation Sequencing has enabled to generate more than 100 billion base pairs per day from one machine. The produced data are randomly fragmented DNA base pair strings, called short reads. Next step for the genetic analysis is the short read mapping, which determines the location of the short reads in the reference genomes. The traditional software tools for the short read mapping are slower than NGS throughput. In this paper, we propose a scalable FPGA system based on the hash index method.
Keyword (in Japanese) (See Japanese page) 
(in English) FPGA / Bioinformatics / Short Read Mapping / Application Acceleration / / / /  
Reference Info. IEICE Tech. Rep., vol. 113, no. 52, RECONF2013-4, pp. 19-24, May 2013.
Paper # RECONF2013-4 
Date of Issue 2013-05-13 (RECONF) 
ISSN Print edition: ISSN 0913-5685  Online edition: ISSN 2432-6380
All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034)
Download PDF RECONF2013-4

Conference Information
Committee RECONF  
Conference Date 2013-05-20 - 2013-05-21 
Place (in Japanese) (See Japanese page) 
Place (in English) Kochi Prefectural Culture Hall 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Reconfigurable Systems, etc. 
Paper Information
Registration To RECONF 
Conference Code 2013-05-RECONF 
Language Japanese 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) FPGA Acceleration of Short Read Mapping 
Sub Title (in English)  
Keyword(1) FPGA  
Keyword(2) Bioinformatics  
Keyword(3) Short Read Mapping  
Keyword(4) Application Acceleration  
1st Author's Name Yoko Sogabe  
1st Author's Affiliation University of Tsukuba (Univ. of Tsukuba)
2nd Author's Name Tsutomu Maruyama  
2nd Author's Affiliation University of Tsukuba (Univ. of Tsukuba)
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Speaker Author-1 
Date Time 2013-05-20 15:50:00 
Presentation Time 25 minutes 
Registration for RECONF 
Paper # RECONF2013-4 
Volume (vol) vol.113 
Number (no) no.52 
Page pp.19-24 
Date of Issue 2013-05-13 (RECONF) 

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