Reconfigurable acceleration of genetic sequence alignment: A survey of two decades of efforts
File(s)
Accepted version
Author(s)
Ng, HC
Liu, S
Luk, W
Type
Conference Paper
Abstract
Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming flexibility and thus has not been commensurately used by practitioners. Therefore, this paper aims to provide a thorough survey of the proposed accelerators by giving a qualitative categorization based on their algorithms and speedup. A comprehensive comparison between work is also presented so as to guide selection for biologist, and to provide insight on future research direction for FPGA scientists.
Date Issued
2017-10-05
Date Acceptance
2017-09-04
Citation
2017 27th International Conference on Field Programmable Logic and Applications (FPL), 2017
ISSN
1946-1488
Publisher
IEEE
Journal / Book Title
2017 27th International Conference on Field Programmable Logic and Applications (FPL)
Copyright Statement
© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Sponsor
Engineering & Physical Science Research Council (E
Commission of the European Communities
Engineering & Physical Science Research Council (E
Grant Number
PO 1553380
671653
516075101 (EP/N031768/1)
Source
2017 27th International Conference on Field Programmable Logic and Applications (FPL)
Publication Status
Published
Start Date
2017-09-04
Finish Date
2017-09-08
Coverage Spatial
Ghent, Belgium