FPGA acceleration of DNA sequencing analysis and storage

Yongpeng Zhang, Linsen Li, Jun Xiao, Yanli Yang, Zexuan Zhu, FQZip: Lossless Reference-Based Compression of Next Generation Sequencing Data in FASTQ Format Springer, Cham. pp. 127- 135 ,(2015) , 10.1007/978-3-319-13356-0_11

Francis P. Russell, Peter D. Duben, Xinyu Niu, Wayne Luk, T.N. Palmer, Architectures and Precision Analysis for Modelling Atmospheric Variables with Chaotic Behaviour field-programmable custom computing machines. pp. 171- 178 ,(2015) , 10.1109/FCCM.2015.52

Yoko Sogabe, Tsutomu Maruyama, A variable length hash method for faster short read mapping on FPGA field programmable logic and applications. pp. 1- 6 ,(2015) , 10.1109/FPL.2015.7293938

Sebastian Wandelt, Ulf Leser, FRESCO: Referential Compression of Highly Similar Sequences IEEE/ACM Transactions on Computational Biology and Bioinformatics. ,vol. 10, pp. 1275- 1288 ,(2013) , 10.1109/TCBB.2013.122

Valentí Moncunill, Santi Gonzalez, Sílvia Beà, Lise O Andrieux, Itziar Salaverria, Cristina Royo, Laura Martinez, Montserrat Puiggròs, Maia Segura-Wang, Adrian M Stütz, Alba Navarro, Romina Royo, Josep L Gelpí, Ivo G Gut, Carlos López-Otín, Modesto Orozco, Jan O Korbel, Elias Campo, Xose S Puente, David Torrents, None, Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads Nature Biotechnology. ,vol. 32, pp. 1106- 1112 ,(2014) , 10.1038/NBT.3027

Edward B. Fernandez, Jason Villarreal, Stefano Lonardi, Walid A. Najjar, FHAST: FPGA-Based Acceleration of Bowtie in Hardware IEEE/ACM Transactions on Computational Biology and Bioinformatics. ,vol. 12, pp. 973- 981 ,(2015) , 10.1109/TCBB.2015.2405333

Jing Zhang, Heshan Lin, Pavan Balaji, Wu-Chun Feng, Optimizing burrows-wheeler transform-based sequence alignment on multicore architectures ieee acm international symposium cluster cloud and grid computing. pp. 377- 384 ,(2013) , 10.1109/CCGRID.2013.67

Andrew Canis, Jongsok Choi, Mark Aldham, Victor Zhang, Ahmed Kammoona, Jason H. Anderson, Stephen Brown, Tomasz Czajkowski, LegUp Proceedings of the 19th ACM/SIGDA international symposium on Field programmable gate arrays - FPGA '11. pp. 33- 36 ,(2011) , 10.1145/1950413.1950423

Nils Homer, Barry Merriman, Stanley F. Nelson, BFAST: An Alignment Tool for Large Scale Genome Resequencing PLoS ONE. ,vol. 4, pp. e7767- 12 ,(2009) , 10.1371/JOURNAL.PONE.0007767

KC Allen Chan, Peiyong Jiang, Carol WM Chan, Kun Sun, John Wong, Edwin P Hui, Stephen L Chan, Wing Cheong Chan, David SC Hui, Simon SM Ng, Henry LY Chan, Cesar SC Wong, Brigette BY Ma, Anthony TC Chan, Paul BS Lai, Hao Sun, Rossa WK Chiu, YM Dennis Lo, None, Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 18761- 18768 ,(2013) , 10.1073/PNAS.1313995110