Accelerating the Next Generation Long Read Mapping with the FPGA-Based System

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 11; no. 5; pp. 840 - 852
• Main Authors: Chen, Peng, Wang, Chao, Li, Xi, Zhou, Xuehai
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.09.2014; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Acceleration; Algorithms; Alignment; Bioinformatics; Biology; Computer programs; Equipment Design; Genomics; Genomics - instrumentation; Genomics - methods; High-Throughput Nucleotide Sequencing - instrumentation; High-Throughput Nucleotide Sequencing - methods; Humans; Indexes; Mapping; Platforms; Sequence Alignment - instrumentation; Sequence Alignment - methods; Sequence Analysis, DNA - instrumentation; Sequence Analysis, DNA - methods; Sequencing; Sequential analysis; Software; Software algorithms; State of the art; Smith-Waterman; long read mapping; BWA-SW; hardware acceleration; Sequence alignment
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2014.2326876

To compare the newly determined sequences against the subject sequences stored in the databases is a critical job in the bioinformatics. Fortunately, recent survey reports that the state-of-the-art aligners are already fast enough to handle the ultra amount of short sequence reads in the reasonable time. However, for aligning the long sequence reads (>400 bp) generated by the next generation sequencing (NGS) technology, it is still quite inefficient with present aligners. Furthermore, the challenge becomes more and more serious as the lengths and the amounts of the sequence reads are both keeping increasing with the improvement of the sequencing technology. Thus, it is extremely urgent for the researchers to enhance the performance of the long read alignment. In this paper, we propose a novel FPGA-based system to improve the efficiency of the long read mapping. Compared to the state-of-the-art long read aligner BWA-SW, our accelerating platform could achieve a high performance with almost the same sensitivity. Experiments demonstrate that, for reads with lengths ranging from 512 up to 4,096 base pairs, the described system obtains a 10x -48x speedup for the bottleneck of the software. As to the whole mapping procedure, the FPGA-based platform could achieve a 1.8x -3:3x speedup versus the BWA-SW aligner, reducing the alignment cycles from weeks to days.