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Liu et al., 2017 - Google Patents

A customized many-core hardware acceleration platform for short read mapping problems using distributed memory interface with 3D–stacked architecture

Liu et al., 2017

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Document ID
12915486276322278181
Author
Liu P
Hemani A
Paul K
Weis C
Jung M
Wehn N
Publication year
Publication venue
Journal of Signal Processing Systems

External Links

Snippet

Abstract Rapidly developing Next Generation Sequencing technologies produce huge amounts of short reads that consisting randomly fragmented DNA base pair strings. Assembling of those short reads poses a challenge on the mapping of reads to a reference …
Continue reading at link.springer.com (HTML) (other versions)

Classifications

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    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30312—Storage and indexing structures; Management thereof
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30386—Retrieval requests
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/50—Computer-aided design
    • G06F17/5009—Computer-aided design using simulation
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F15/00—Digital computers in general; Data processing equipment in general
    • G06F15/16—Combinations of two or more digital computers each having at least an arithmetic unit, a programme unit and a register, e.g. for a simultaneous processing of several programmes
    • G06F15/163—Interprocessor communication
    • G06F15/173—Interprocessor communication using an interconnection network, e.g. matrix, shuffle, pyramid, star, snowflake
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/50—Computer-aided design
    • G06F17/5068—Physical circuit design, e.g. layout for integrated circuits or printed circuit boards
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F12/00—Accessing, addressing or allocating within memory systems or architectures
    • G06F12/02—Addressing or allocation; Relocation
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F13/00—Interconnection of, or transfer of information or other signals between, memories, input/output devices or central processing units
    • G06F13/14—Handling requests for interconnection or transfer
    • G06F13/16—Handling requests for interconnection or transfer for access to memory bus
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F9/00—Arrangements for programme control, e.g. control unit
    • G06F9/06—Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/06—Digital input from or digital output to record carriers, e.g. RAID, emulated record carriers, networked record carriers
    • G06F3/0601—Dedicated interfaces to storage systems
    • G06F3/0628—Dedicated interfaces to storage systems making use of a particular technique
    • G—PHYSICS
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    • G06F11/00—Error detection; Error correction; Monitoring

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