Date of Award


Degree Name

Master of Science in Engineering


Electrical and Computer Engineering

First Advisor

Dr. Fahad Saeed

Second Advisor

Dr. Elise de Doncker

Third Advisor

Dr. Janos Grantner


FPGA, High Performance Computing, short read alignment. DNA sequencins. Bioinformatics

Access Setting

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.