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


The alignment of several short DNA fragments to a giant genome may be a terribly important facet of the trendy computational biology. But, software-primarily based DNA sequence alignment takes many hours to finish. This paper proposes an FPGA-based mostly hardware accelerator to reduce the alignment time. We tend to apply a knowledge encoding theme that reduces the info size by 96 %, and propose a pipelined hardware decoder to decode the info. We have a tendency to additionally style customized knowledge paths to efficiently use the restricted bandwidth of the DDR3 memories. The proposed accelerator can align a few hundred million short DNA fragments in an hour by using eighty processing parts in parallel. The proposed accelerator has the identical mapping quality compared to the software-primarily based strategies.

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