Hardware-Acceleration of Short-Read Alignment Based on the Burrows-Wheeler Transform

The alignment of millions of short DNA fragments to a large genome is a very important aspect of the modern computational biology. However, software-based DNA sequence alignment takes many hours to complete. This paper proposes an FPGA-based hardware accelerator to reduce the alignment time. We apply a data encoding scheme that reduces the data size by 96 percent, and propose a pipelined hardware decoder to decode the data. We also design customized data paths to efficiently use the limited bandwidth of the DDR3 memories. The proposed accelerator can align a few hundred million short DNA fragments in an hour by using 80 processing elements in parallel. The proposed accelerator has the same mapping quality compared to the software-based methods.