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Thread: FPGA accelerated BWT

  1. #1
    Member m^2's Avatar
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    more details

    see also

    Convey Computer ? Burrows-Wheeler Aligner Personality

    The popular Burrows-Wheeler Aligner (BWA) application
    is used for aligning relatively short nucleotide sequences
    against a long reference sequence.

    The Convey implementation leverages the unique hybrid-core
    architecture to move performance-critical regions of the
    application into hardware, greatly accelerating the application
    while reducing space, power, and maintenance requirements.

    Next-generation sequencing instruments generate
    enormous quantities of raw sequence data.

    Sifting through this data is important??identifying meaningful variants is critical for biological insight and clinical guidance, such as cancer tumor profiling??however, in such volumes it becomes tremendously difficult. To identify SNPs, indels, and CNVs, the raw sequence data needs to be mapped against known reference sequences composed of billions of base pairs. One of the preferred aligner tools for mapping the short reads produced by these instruments is the Burrows-Wheeler Aligner (BWA) (Li & Durbin, 2009).

    BWA uses a Burrows-Wheeler transform to index the reference genome, reducing the space that must be searched and the time to map a sequence. BWA performs large numbers of relatively simple operations on a sparse data structure−operations which are problematic for a commodity system, but are ideal for the Convey hybrid-core architecture. Convey?s BWA personality is designed to accelerate the alignment step of the BWA pipeline, and can achieve a ten-fold performance improvement over BWA run on commodity servers.


    Convey?s solution starts with its innovative hybrid- core platforms?the HC-1 and the HC-1 ex ?that use reconfigurable technology and a parallel memory subsystem to accelerate applications and lower the cost of ownership. Convey?s hybrid-core architecture pairs classic Intel ? x86 microprocessors with a coprocessor comprised of FPGAs. Particular algorithms?such as BWA?are implemented as hardware modules that are loadable onto the FPGAs at runtime to accelerate the applications that use them.


    The combination of BWA?s inherent strengths with Convey?s hybrid-core implementation produces important benefits for researchers and clinicians.

    ? Speed in the clinic:

    Delivering modern personalized medicine?increasingly supported by molecular techniques such as cancer tumor profiling?depends upon being able to rapidly and accurately interpret next-generation sequencing data.
    The speed of Convey?s BWA accelerates the pursuit of molecular medicine.

    ? Research productivity:

    Declining sequencing costs are spurring a jump in the number of reference genomes available, stimulating more sequencing work to mine those reference genomes. Convey?s BWA personality enables researchers to work faster on particular projects and to tackle more projects simultaneously.

    ? Ease of use:

    Convey?s BWA is optimized to emphasize ease of use; it uses the same command lines and arguments as the original BWA algorithm.

    ? Departmental-scale solution:

    Convey?s systems are proving to be powerful departmental computer solutions, allowing researchers to solve ?big data? problems locally?without having to copy enormous data sets to, or schedule time on, a large shared cluster.

    ? Improved TCO:

    Convey systems are less expensive to operate. For example, eight Convey HC-1 ex systems provide the same performance as 120 12-core
    commodity servers, while using 75 percent less floor space and 79 percent less power. Over three years, price, power, and space improvements provide a 60*% reduction in total cost of ownership
    (Based on Convey benchmarks - throughput of an overall BWA workflow).

    Reference mapping is a powerful tool for deciphering genomes for basic knowledge and practical medical benefit. Convey?s BWA personality helps researchers perform this function substantially faster and more cost- effectively. Convey?s innovative hybrid-core computer system marries the low cost and simple programming model of a commodity system with the performance of a customized hardware architecture.

    For more information:

    Convey Computer Corporation
    1302 E.Collins Boulevard, Richardson, Texas 75081

    phone: 214.666.6024 - toll Free: 866.338.1768
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  3. #3
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    How it compares to libbsc?

  4. #4
    Member m^2's Avatar
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    Quote Originally Posted by Piotr Tarsa View Post
    How it compares to libbsc?
    Buy me the machine and I'll gladly test it. ^^

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