Genome Alignment

Scientific researches at many fields need computational power sometimes even more than industrial applications. To demonstrate the power of FPGA, Aldec and Indian Institute of Science faculty enterprise, ReneLife, implemented algorithm of ReneGENE for accurate genome alignment on Aldec’s HES-HPC FPGA-based accelerator.

 

ReneGENE offered on HES-HPC as AccuRA, for accurate, and ultra-fast big data mapping and alignment of DNA short-reads from the Next Generation Sequencing (NGS) platforms, with full coverage of the genome (million to billion bases long), including repeat regions. The technology, devoid of heuristics can precisely align the DNA reads against a reference genome at a single nucleotide resolution. As genomics permeates the entire landscape of biology, including biomedicine and therapeutics, ReneGENE creates a genomic highway that significantly contributes to reduce the time from sample to information without compromising on accuracy, critical for lifesaving medicare applications, biotechnology product development and forensics.

 

 

genome alignment

  • Aldec HES-HPC is ~10x faster than GMAccS, the single GPU OpenCL
  • Aldec HES-HPC is ~26x faster than CUSHAW, the open source single GPU CUDA
  • GMAccS demonstrates a speedup over 150x compared to the standard heuristic aligners like BFAST, so AccuRA is several orders faster than the competitors
  • HES-HPC has more available FPGA resource for more hardware kernels, possible to put up to 6 kernels in one FPGA

 

Main Features

  • Fully streaming, multithreaded, parallel dynamic programming in hardware eliminates memory bottleneck and storage issues
  • Reduces computing and I/O burden on the host significantly
  • Achieves short read mapping in minimum deterministic time
  • Highly accurate and precise SRM solution
  • Fastest genome aligner in the market
  • Scalable at multiple levels of design granularity, massively parallel solution
  • Scalable in data size, ranging from genome sizes of millions to billions
  • ReneGENE AccuRA most cost-effective solution. The customer will incur less than one percent of his monthly expenditures for ReneLife-Aldec solution compared to conventional cluster, and also save time due to accelerated performance.
  • The results of the alignment from ReneGENE is available in a standard format, called .SAM or its equivalent binary known as .BAM, which can be processed by the downstream analysis tools in any lab across the globe.
  • End-users include
    • NGS OEMs
    • Large research groups
    • Medical research groups and hospitals
    • Small research groups and diagnostics labs
      forensics
    • Individuals like clinicians

 

Solution Contents

  • ReneGENE software application
  • AccuRA system running on HES-HPC

 

Partner

ReneLife

ReneLife is a technology start-up, launched as a faculty enterprise of the Indian Institute of Science, in the area of Life Sciences. ReneLife is devoted to providing cutting-edge hardware-software co-designed accelerated solutions. It has made a start by developing ReneGENE - a proprietary core technology, for accelerated accurate alignment of short reads from Next Generation Sequencing (NGS) platforms through massively parallel and scalable realizations. The objective of the company is to bring new affordable and commodity scale products and solutions to market, that extends the frontiers of precision and targeted medicine.

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