GPU Accelerated API for Alignment of Genomics Sequencing Data

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review

5 Citations (Scopus)

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 library (GASAL) for pairwise sequence alignment of DNA and RNA sequences. The GASAL library provides 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 200x faster than the NVBIO approach. Overall on Tesla K40c GASAL is 10-14x faster than 28 Intel Xeon cores and 3-4x faster than NVBIO with a query length of 100 bases. The library provides easy to use APIs to allow integration into various bioinformatics tools.
Original languageEnglish
Title of host publication2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
EditorsX. Hu, C.R. Shyu, Y. Bromberg, J. Gao, Y. Gong, D. Korkin, I. Yoo, J.H. Zheng
Place of PublicationDanvers
PublisherIEEE
Pages510-515
Number of pages6
ISBN (Electronic)978-1-5090-3050-7
ISBN (Print)978-1-5090-3051-4
DOIs
Publication statusPublished - Nov 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine - Kansas City, United States
Duration: 13 Nov 201716 Nov 2017

Conference

Conference2017 IEEE International Conference on Bioinformatics and Biomedicine
Abbreviated titleIEEE BIBM 2017
CountryUnited States
CityKansas City
Period13/11/1716/11/17

Keywords

  • sequence alignment
  • GPU acceleration
  • software API
  • NGS

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