NDLI: Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

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ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 10

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 9

Issue 4(Regular Papers and Special Section on Field Programmable Gate Arrays (FPGA) 2015), September 2016

Issue 3(Special Issue on Reconfigurable Components with Source Code), September 2016

Introduction to Special Issue on Reconfigurable Components with Source Code

Open-Source Variable-Precision Floating-Point Library for Major Commercial FPGAs

The Unified Accumulator Architecture: A Configurable, Portable, and Extensible Floating-Point Accumulator

Modular Switched Multiported SRAM-Based Memories

A Parallel Sliding-Window Generator for High-Performance Digital-Signal Processing on FPGAs

Optimizing Soft Vector Processing in FPGA-Based Embedded Systems

Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

Issue 2(Special Section on RAW2014), February 2016

Issue 1(Special Section on the 2014 International Symposium on Applied Reconfigurable Computing), November 2015

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 8

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 7

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 6

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 5

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 4

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 3

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 2

ACM Transactions on Reconfigurable Technology and Systems (TRETS) : Volume 1

Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

Content Provider	ACM Digital Library
Author	Requa, Michael Kimura, Motoki Kastner, Ryan Anantharaman, Thomas Meng, Pingfan Jacobsen, Matthew Dergachev, Vladimir
Copyright Year	2016
Abstract	De novo assembly is a widely used methodology in bioinformatics. However, the conventional short-read-based de novo assembly is incapable of reliably reconstructing the large-scale structures of human genomes. Recently, a novel optical label-based technology has enabled reliable large-scale de novo assembly. Despite its advantage in large-scale genome analysis, this new technology requires a more computationally intensive alignment algorithm than its conventional counterpart. For example, the runtime of reconstructing a human genome is on the order of 10,000 hours on a sequential CPU. Therefore, in order to practically apply this new technology in genome research, accelerated approaches are desirable. In this article, we present three different accelerated approaches, multicore CPU, GPU, and FPGA. Against the sequential software baseline, our multicore CPU design achieved an 8.4× speedup, while the GPU and FPGA designs achieved 13.6× and 115× speedups, respectively. We also discuss the details of the design space exploration of this new assembly algorithm on these three different devices. Finally, we compare these devices in performance, optimization techniques, prices, and design efforts.
Starting Page	1
Ending Page	21
Page Count	21
File Format	PDF
ISSN	19367406
e-ISSN	19367414
DOI	10.1145/2840811
Volume Number	9
Issue Number	3
Journal	ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2016-09-03
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	FPGA GPU Genome Acceleration De novo assembly
Content Type	Text
Resource Type	Article
Subject	Computer Science

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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Hardware Accelerated Alignment Algorithm for Optical Labeled Genomes

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