GPU accelerated API for alignment of genomics sequencing data

Abstract

Sequence alignment is a core step in the processing of DNA and RNA sequencing data. In this paper, we present a high performance GPU accelerated set of APIs (GASAL) for pairwise sequence alignment of DNA and RNA sequences. The GASAL APIs provide accelerated kernels for local, global as well as semi-global alignment, allowing the computation of the alignment score, and optionally the start and end positions of the alignment. GASAL outperforms the fastest CPU-optimized SIMD implementations such as SSW and Parasail. It also outperforms NVBIO, NVIDIA's own CUDA library for sequence analysis of high-throughput sequencing data. GASAL uses the unique approach of also performing the sequence packing on GPU, which is over 200× faster than the NVBIO approach. Overall on Tesla K40c GASAL is 10–14× faster than 28 Intel Xeon cores and 3–4× faster than NVBIO with a query length of 100 bases. The APIs are included in an easy to use library to allow integration into various bioinformatics tools.