A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation


This paper presents an FPGA based DNA comparison platform that can be run concurrently with the sensing phase of DNA sequencing and shortens the time needed for de novo DNA assembly. A hybrid overlap looking out algorithm is applied which is scalable and can cope with incremental detection of recent bases. To handle the unfinished data set which gradually will increase throughout sequencing time, all-against-all comparisons are softened into successive window-against-window comparison phases and executed employing a novel dynamic suffix comparison algorithm combined with a partitioned dynamic programming method. The whole system has been designed to facilitate parallel processing in hardware, that permits real-time comparison and full scalability and a decrease in the quantity of computations required. A base pair comparison rate of fifty one.two G/s is achieved when implemented on an FPGA with successful DNA comparison when using knowledge sets from real genomes.

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