Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

In this paper we present an implementation of the Smith-Waterman algorithm. The implementation is done in OpenCL and targets high-end GPUs. This implementation is capable of computing similarity indexes between reference and query sequences. The implementation is designed for the sequence alignment paths calculation. In addition, it is capable of handling very long reference sequences (in the order of millions of nucleotides), a requirement for the target application in cancer research. Performance compares favorably against CPU, being on the order of 9 - 130 times faster, 3 times faster than the CUDA-enabled CUDASW++v2.0 for medium sequences or larger. Additionally, it is on par with Farrar´s performance, but with less constraints in sequence length.