Architecture Design of the Parallel Processing Element and Interconnection Network for De Novo Sequence Assembly
Date Issued
2012
Date
2012
Author(s)
Huang, Yu-Long
Abstract
This thesis researches into the topic of DNA de novo sequence assembly for a novel parallel hardware architecture design including the improvement of the algorithm, preliminary software simulation and the final result of circuit design.
The genome sequences contained in beings are crucial for the knowledge of species. Because the sizes of genome data are such huge, it still consumes a lot of time with the emergence of Next Generation Sequencing. Currently, one of the bottlenecks is the limited bandwidth for data transfer, which greatly slows sequencing speeds. Hence we made an effort in improving this situation.
In this thesis, we purpose a parallel DNA de novo sequence assembly algorithm. Based on the algorithm, processing elements (PEs) are designed and connected to the proposed interconnection network so that huge genome data could be transferred efficiently between PEs. Compared to previous approaches, it has advantages in both bandwidth and parallelism. Therefore, the sequencing process is much faster than those conventional approaches. As verified by software simulations, we can guarantee the quality of the solutions. Also, we have implemented the PE with TSMC 90 nm process. According to the simulation results, the hardware can be operated at frequency of 100 MHz and speed up about 10 times when compared to previous software approaches.
Subjects
De novo assembly
Interconnection network
Parallel processing element
Type
thesis
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