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A Customized Many-Core Hardware Acceleration Platform for Short Read Mapping Problems Using Distributed Memory Interface with 3D-Stacked Architecture
KTH, School of Information and Communication Technology (ICT), Electronics.
KTH, School of Information and Communication Technology (ICT), Electronics.ORCID iD: 0000-0003-0565-9376
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2017 (English)In: Journal of Signal Processing Systems, ISSN 1939-8018, E-ISSN 1939-8115, Vol. 87, no 3, 327-341 p.Article in journal (Refereed) Published
Abstract [en]

Rapidly developing Next Generation Sequencing technologies produce huge amounts of short reads that consisting randomly fragmented DNA base pair strings. Assembling of those short reads poses a challenge on the mapping of reads to a reference genome in terms of both sensitivity and execution time. In this paper, we propose a customized many-core hardware acceleration platform for short read mapping problems based on hash-index method. The processing core is highly customized to suite both 2-hit string matching and banded Smith-Waterman sequence alignment operations, while distributed memory interface with 3D-stacked architecture provides high bandwidth and low access latency for highly customized dataset partitioning and memory access scheduling. Conformal with original BFAST program, our design provides an amazingly 45,012 times speedup over software approach for single-end short reads and 21,102 times for paired-end short reads, while also beats similar single FPGA solution for 1466 times in case of single end reads. Optimized seed generation gives much better sensitivity while the performance boost is still impressive.

Place, publisher, year, edition, pages
Springer, 2017. Vol. 87, no 3, 327-341 p.
Keyword [en]
Accelerator architectures, Application specific integrated circuits, Bioinformatics, Computational biology, Coprocessors, Three-dimensional integrated circuits
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
URN: urn:nbn:se:kth:diva-208228DOI: 10.1007/s11265-016-1204-8ISI: 000399451800005Scopus ID: 2-s2.0-85001022032OAI: oai:DiVA.org:kth-208228DiVA: diva2:1116020
Note

QC 20170627

Available from: 2017-06-27 Created: 2017-06-27 Last updated: 2017-06-27Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
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