Date of Award
Master of Science in Engineering
Electrical and Computer Engineering
Dr. Fahad Saeed
Dr. Elise de Doncker
Dr. Janos Grantner
Masters Thesis-Open Access
Due to modern DNA sequencing technologies vast amount of short DNA sequences known as short-reads is generated. Biologists need to be able to align the short-reads to a reference genome to be able to make scientific use of the data. Fast and accurate short-read aligner programs are needed to keep up with the pace at which this data is generated. Field Programmable Gate Arrays have been widely used to accelerate many data-intensive bioinformatics applications.
Burrows-Wheeler Transform has been used in the theory of string matching which has led to the development of many short-read alignment programs. This thesis presents a hardware implementation of Burrows-Wheeler Aligner on a Field Programmable Gate Array (FPGA). We specifically concentrated on the exact match of the short-reads and our implementation resulted in execution that is 82X faster than that of a CPU implementation.
Qader, Dana Abdul, "A High Performance Architecture for an Exact Match Short-Read Aligner Using Burrows-Wheeler Aligner on FPGAs" (2015). Master's Theses. 668.