G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads

Bulletin of the Polish Academy of Sciences. Technical Sciences

J. BlazewiczInstitute of Computing Science, Pozna? University of Technology, Pozna?, PolandInstitute of Bioorganic Chemistry, Polish Academy of Sciences, Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar¹  P. WojciechowskiInstitute of Computing Science, Pozna? University of Technology, Pozna?, PolandLuxembourg Centre for Systems Biomedicine, University of Luxembourg, LuxembourgOther articles by this author:De Gruyter OnlineGoogle Scholar¹  M. KierzynkaCorresponding authorInstitute of Computing Science, Pozna? University of Technology, Pozna?, PolandPozna? Supercomputing and Networking Center, Pozna?, PolandEmailOther articles by this author:De Gruyter OnlineGoogle Scholar¹  P. GawronInstitute of Computing Science, Pozna? University of Technology, Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar¹  W. FrohmbergInstitute of Computing Science, Pozna? University of Technology, Pozna?, PolandOther articles by this author:De Gruyter OnlineGoogle Scholar¹ 

[1] Institute of Computing Science, Pozna? University of Technology, Pozna?, Poland

关键词: Keywords : DNA assembly preprocessing;    sequence alignment;    GPU computing;   

DOI  :  10.2478/bpasts-2013-0106

学科分类：工程和技术（综合）

来源: Polska Akademia Nauk * Centrum Upowszechniania Nauki / Polish Academy of Sciences, Center for the Advancement of Science

【 摘 要 】

DNA/RNA sequencing has recently become a primary way researchers generate biological data for further analysis. Assembling algorithms are an integral part of this process. However, some of them require pairwise alignment to be applied to a great deal of reads. Although several efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units), none of them directly targets high-throughput sequencing data. As a result, a need arose to create software that could handle such data as effectively as possible. G-DNA (GPU-based DNA aligner) is the first highly parallel solution that has been optimized to process nucleotide reads (DNA/RNA) from modern sequencing machines. Results show that the software reaches up to 89 GCUPS (Giga Cell Updates Per Second) on a single GPU and as a result it is the fastest tool in its class. Moreover, it scales up well on multiple GPUs systems, including MPI-based computational clusters, where its performance is counted in TCUPS (Tera CUPS).

【 授权许可】

Unknown