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Hardware Accelerated Novel Optical De Novo Assembly for Large-Scale Genomes Pingfan Meng∗† , Matthew Jacobsen∗† , Motoki Kimura∗‡ , Vladimir Dergachev§ , Thomas Anantharaman§ , Michael Requa§ and Ryan Kast
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Document Date: 2014-06-30 10:30:54


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File Size: 1,67 MB

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GPU / /

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Facility

Engineering University of California / /

IndustryTerm

assembly algorithm / intensive alignment algorithm / conventional shortread technology / parallel computing power / optical based technology / pre-processing algorithm / identical boundary score algorithm / pair-wise alignment algorithm / nanochannel device / software implementations / performance solution / short-read technology / assembly tool / sequential software baseline / software pipeline / maximum score search kernel / alignment algorithm / accelerated solution / /

Organization

Accelerated Novel Optical De Novo Assembly for Large-Scale Genomes Pingfan Meng∗† / Department of Computer Science / Hardware Accelerated Novel Optical De Novo Assembly for Large-Scale Genomes Pingfan Meng∗† / University of California / San Diego / /

Person

Vladimir Dergachev / Motoki Kimura / Matthew Jacobsen / Ryan Kastner / Michael Requa / Thomas Anantharaman / /

Position

correspondent / /

Product

High-Level Synthesis / Vivado HLS / performed using High-Level Synthesis / /

ProgrammingLanguage

C++ / /

Technology

Genomics / FPGA / identical boundary score algorithm / bioinformatics / pair-wise alignment algorithm / T-1 / ESIGNS The algorithm / pre-processing algorithm / leftmost 4 columns Algorithm / alignment algorithm / CPU assembly algorithm / computationally intensive alignment algorithm / Smith-Waterman algorithm / shared memory / assembly algorithm / short-read technology / human genome / optical based technology / conventional shortread technology / /

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