Change search
ReferencesLink to record
Permanent link

Direct link
A Many-Core Hardware Acceleration Platform for Short Read Mapping Problem Using Distributed Memory Interface with 3D-stacked Architecture
KTH, School of Information and Communication Technology (ICT), Electronics and Embedded Systems.ORCID iD: 0000-0003-0565-9376
2014 (English)In: 2014 INTERNATIONAL SYMPOSIUM ON SYSTEM-ON-CHIP (SOC)Article in journal (Refereed) Published
Abstract [en]

Next Generation Sequencing technologies produce huge amounts of short reads consisting randomly fragmented DNA base pair strings, while assembling poses a challenge on the mapping of short reads to a reference genome in terms of both sensitivity and execution time. In this paper, we propose a many-core hardware acceleration platform for short read mapping based on hash-index method, which benefit from a distributed memory interface with 3D-stacked architecture for local memory access. Our design provides an amazingly 45012 times speedup over software approach for single end short reads and 21102 times for paired end reads, while also beats similar single FPGA solution for 1466 times in case of single end reads.

Place, publisher, year, edition, pages
IEEE Press, 2014.
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
URN: urn:nbn:se:kth:diva-171032ISI: 000356507900024ISBN: 978-1-4799-6890-9OAI: diva2:841313
16th International Symposium on System-on-Chip (SoC), OCT 28-29, 2014, Tampere, FINLAND

QC 20150713

Available from: 2015-07-13 Created: 2015-07-13 Last updated: 2015-07-13Bibliographically approved

Open Access in DiVA

No full text

Search in DiVA

By author/editor
Liu, PeiHemani, Ahmed
By organisation
Electronics and Embedded Systems
Electrical Engineering, Electronic Engineering, Information Engineering

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 14 hits
ReferencesLink to record
Permanent link

Direct link