An experimental study of an opportunistic index
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Bioinformatics
High Throughput Short Read Alignment via Bi-directional BWT
BIBM '09 Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine
String Matching in Hardware Using the FM-Index
FCCM '11 Proceedings of the 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines
Bioinformatics
Short-Read Mapping by a Systolic Custom FPGA Computation
FCCM '12 Proceedings of the 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines
Accelerating Millions of Short Reads Mapping on a Heterogeneous Architecture with FPGA Accelerator
FCCM '12 Proceedings of the 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines
Hardware Acceleration of Short Read Mapping
FCCM '12 Proceedings of the 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines
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Next generation DNA sequencing machines have been improving at an exceptional rate; the subsequent analysis of the generated sequenced data has become a bottleneck in current systems. This paper explores the use of reconfigurable hardware to accelerate the short read mapping problem, where the positions of millions of short DNA sequences are located relative to a known reference sequence. The proposed design comprises of an alignment processor based on a backtracking variation of the FM-index algorithm. The design represents a full solution to the short read mapping problem, capable of efficient exact and approximate alignment. We use reconfigurable hardware to accelerate the design and find that an implementation targeting the MaxWorkstation performs considerably faster and more energy efficient than current CPU and GPU based software aligners.