Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths

Ahmed, 2015, Heterogeneous hardware/software acceleration of the BWA-MEM DNA alignment algorithm Alpha Data, 2015 Bioplanet.com, 2016 Chang, 2016, The SMEM seeding algorithm acceleration for DNA sequence alignment Chen, 2015 Chen, 2016, When apache spark meets FPGAs: a case study for next-generation DNA sequencing acceleration, 8th USENIX Workshop on Hot Topics in Cloud Computing Di Tucci, 2017, Architectural optimizations for high performance and energy efficient Smith-Waterman implementation on FPGAs using OpenCL, 716 Hasan, 2011, DOPA: GPU-based protein alignment using database and memory access optimizations, BMC Res. Notes, 4, 261, 10.1186/1756-0500-4-261 Highnam, 2015, An analytical framework for optimizing variant discovery from personal genomes, Nat. Commun., 6, 10.1038/ncomms7275 Houtgast, 2015, An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm, Intl. Conf. on Embedded Computer Systems: Architectures, Modeling, and Simulation Houtgast, 2016, GPU-accelerated BWA-MEM genomic mapping algorithm using adaptive load balancing, 130 Houtgast, 2016, Power-efficient accelerated genomic short read mapping on heterogeneous computing platforms Houtgast, 2016, An efficient GPU-accelerated implementation of genomic short read mapping with BWA-MEM Illumina, 2015 Illumina, 2016 Li, H. Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM. arXiv preprint. arXiv:1303.3997. Ligowski, 2009, An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases, IEEE International Symposium on Parallel & Distributed Processing, 2009. IPDPS 2009. IEEE, 1 Liu, 2012, SOAP3: ultra-fast GPU-based parallel alignment tool for short reads, Bioinformatics, 28, 878, 10.1093/bioinformatics/bts061 Liu, 2012, CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform, Bioinformatics, 28, 1830, 10.1093/bioinformatics/bts276 Manavski, 2008, CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinform., 9, S10, 10.1186/1471-2105-9-S2-S10 NVIDIA, 2016 NVIDIA, 2016 Stephens, 2015, Big data: astronomical or genomical?, PLoS Biol., 13, 10.1371/journal.pbio.1002195