Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

Péter Fehér 1 , Ágnes Fülöp 2 , Gergely Debreczeni 3 , Máté Nagy-Egri 4  and György Vesztergombi 5
  • 1 Eötvös Loránd University
  • 2 Eötvös Loránd University
  • 3 Wigner Institute
  • 4 Wigner Institute
  • 5 Wigner Institute and Eötvös Loránd University


With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays) technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation) errors.

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