GateKeeper

GateKeeper is a hardware accelerator designed to quickly filter out most incorrect locations in pre-alignment using Field-Programmable Gate Arrays (FPGAs). This design can achieve up to 90-fold and 130-fold speedups over Adjacency Filter and Shifted Hamming Distance (SHD), respectively, while maintaining an accuracy of >96%. Adding GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.

Topic

Sequencing;Mapping;Sequence analysis

Detail

  • Operation: Read mapping

  • Software interface: Command-line user interface

  • Language: -

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: National Institutes of Health (NIH), a Marie Curie Career Integration Grant under the Seventh Framework Programme, the Scientific and Technological Research Council of Turkey, under the TUBITAK 2215 program.

  • Input: -

  • Output: -

  • Contact: Mohammed Alser mohammedalser@bilkent.edu.tr, Can Alkan calkan@cs.bilkent.edu.tr, Onur Mutlu onur.mutlu@inf.ethz.ch

  • Collection: -

  • Maturity: -

Publications

  • GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.
  • Alser M, et al. GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. 2017; 33:3355-3363. doi: 10.1093/bioinformatics/btx342
  • https://doi.org/10.1093/bioinformatics/btx342
  • PMID: 28575161
  • PMC: PMC5860160

Download and documentation

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