NDLI: Heterogeneous Cloud Framework for Big Data Genome Sequencing

Content Provider	IEEE Xplore Digital Library
Author	Wang, C. Li, X. Chen, P. Wang, A. Zhou, X. Yu, H.
Copyright Year	2004
Abstract	The next generation genome sequencing problem with short (long) reads is an emerging field in numerous scientific and big data research domains. However, data sizes and ease of access for scientific researchers are growing and most current methodologies rely on one acceleration approach and so cannot meet the requirements imposed by explosive data scales and complexities. In this paper, we propose a novel FPGA-based acceleration solution with MapReduce framework on multiple hardware accelerators. The combination of hardware acceleration and MapReduce execution flow could greatly accelerate the task of aligning short length reads to a known reference genome. To evaluate the performance and other metrics, we conducted a theoretical speedup analysis on a MapReduce programming platform, which demonstrates that our proposed architecture have efficient potential to improve the speedup for large scale genome sequencing applications. Also, as a practical study, we have built a hardware prototype on the real Xilinx FPGA chip. Significant metrics on speedup, sensitivity, mapping quality, error rate, and hardware cost are evaluated, respectively. Experimental results demonstrate that the proposed platform could efficiently accelerate the next generation sequencing problem with satisfactory accuracy and acceptable hardware cost.
Sponsorship	IEEE Computer Society
Starting Page	166
Ending Page	178
Page Count	13
File Size	1205536
File Format	PDF
ISSN	15455963
Volume Number	12
Issue Number	1
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Bioinformatics Genomics Field programmable gate arrays Sequential analysis Hardware Acceleration Computer architecture
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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