FPGA-based acceleration platform and design method for gene sequencing string matching algorithm

Abstract

The invention discloses an FPGA-based acceleration platform and a design method for a gene sequencing string matching algorithm. The acceleration platform includes a PS (Program System) end and a PL (Program Logic) end, and the PS end includes a general-purpose processor and a DRAM to complete the software-side code operation and control of a hardware part, the PL end contains a plurality of IP cores that can be solidified according to requirements to achieve corresponding tasks. First, the general-purpose processor writes string data into the DRAM, and then the FPGA reads the string data fromthe DRAM and starts calculation, and the calculation result is written into the DRAM, and finally the general-purpose processor reads the matching result from the DRAM. The accelerator of the invention deploys multiple independent IP cores for calculation on the FPGA and the IP cores run in a pipeline mode, so that programmers without hardware knowledge can easily obtain good performance by usingexisting FPGA resources.

Description

technical field [0001] The invention relates to a hardware acceleration platform for a gene sequencing algorithm, in particular to an FPGA-based acceleration platform and a design method for a gene sequencing string matching algorithm with good versatility and high flexibility. Background technique [0002] There are many methods of gene sequencing. But no matter how different these methods are in their implementation, they all rely on the principle of DNA replication for their design. DNA replication is simply the process of self-reproduction of DNA. During replication, DNA slowly opens the double-stranded structure, and under the action of various guide enzymes, it is divided into two single strands and generates new matching short strands. Afterwards, the free bases in the nucleus will be added to the newly generated short chains under the action of a series of enzymes to slowly extend the short chains. At the end of replication, the original double-strand DNA is compl...

AI Technical Summary

Problems solved by technology

[0009] To sum up, based on the FPGA platform, it is an attractive choice to design a dedicated hardware accelerator structure from the underlying hardware level to accelerate gene sequencing, but the development of FPGA requires certain experience in hardware design. Because of this, FPGA will Many software programmers are turned away

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