GPU Acceleration of DNA Alignment Algorithms of Long Reads for DNA Assembly

Third generation sequencing machines produce reads with tens of thousands of base pairs.<br/>To perform de novo assembly, all reads must be compared with every other read to find overlaps.<br/>Finding overlaps with the optimal Smith-Waterman is not feasible, since the complexity of Smith-Waterman is quadratic with the length of the reads.<br/...

Low-Cost Smith-Waterman Acceleration

Due to advancing technology, genetic sequencing has become cheaper over the years. This has caused the demand for computational power to grow even faster than Moore's law. To remedy this problem, we analyzed low-cost hardware solutions to parallelize the computational part of the genetic sequencing. We proposed a novel method for calculating the...