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

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...