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GPU based Eulerian Assembly of Genomes

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dc.contributor.advisor Rangwala, Huzefa
dc.contributor.author Mahmood, Syed Faraz
dc.creator Mahmood, Syed Faraz
dc.date 2012-12-04
dc.date.accessioned 2013-02-18T17:32:09Z
dc.date.available NO_RESTRICTION en_US
dc.date.available 2013-02-18T17:32:09Z
dc.date.issued 2013-02-18
dc.identifier.uri https://hdl.handle.net/1920/8013
dc.description.abstract Advances in sequencing technologies have revolutionized the eld of genomics by providing cost e ective and high throughput solutions. In this paper, we develop a parallel sequence assembler implemented on general purpose graphic processor units (GPUs). Our work was largely motivated by a growing need in the genomic community for sequence assemblers and increasing use of GPUs for general purpose computing applications. We investigated the implementation challenges, and possible solutions for a data parallel approach for sequence assembly. We implemented an Eulerian-based sequence assembler (GPU-Euler) on the nVidia GPUs using the CUDA programming interface. GPU-Euler was benchmarked on three bacterial genomes using input reads representing the new generation of sequencing approaches. Our empirical evaluation showed that GPU-Euler produced lower run times, and comparable performance in terms of contig length statistics to other serial assemblers. We were able to demonstrate the promise of using GPUs for genome assembly, a computationally intensive task. An error correction step was also incorporated into GPU-Euler to be able to process reads containing some errors. Error correction output was benchmarked on simulated read on three bacterial genomes with different read length.
dc.language.iso en en_US
dc.subject sequence assembly en_US
dc.subject Euler Tour en_US
dc.subject GPU en_US
dc.subject error correction en_US
dc.subject CUDA en_US
dc.subject spectral alignment en_US
dc.title GPU based Eulerian Assembly of Genomes en_US
dc.type Thesis en
thesis.degree.name Master of Science in Computer Science en_US
thesis.degree.level Master's en
thesis.degree.discipline Computer Science en
thesis.degree.grantor George Mason University en


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