Whole genome sequencing data calculation interpretation method

Abstract

The invention discloses a whole genome sequencing data calculation interpretation method, which comprises the following implementation steps that: inputting reference whole genome data used for whole genome sequencing and organic sequencing sample data, and carrying out preprocessing; calling an FPGA (Field Programmable Gate Array) by a CPU (Central Processing Unit) to be accelerated to compare sequencing sample reliable data with the reference whole genome data with an index to obtain a comparison result with a repeated sign and the index; calling the FPGA and a GPU (Graphics Processing Unit) by the CPU to be accelerated to carry out genome reassembling on the sequencing sample reliable data, and carrying out variant identification recognition on the comparison result with the repeated label and the index; and calling the GPU and a DSP (Digital Signal Processor) by the CPU to be accelerated to carry out visual processing, and calling a deep learning model realized by hardware on the FPGA by the CPU to carry out the analysis and the mining of the whole genome and a variant function on the basis of a visual processing result. By use of the method, the GPU, DSP and FPGA processors can be comprehensively utilized for acceleration, and the method has the advantages of being quick, real-time, accurate in penetration, popular and easy in understanding and varied in forms.

Description

technical field [0001] The invention relates to gene sequencing technology, in particular to a calculation and interpretation method for whole genome sequencing data. Background technique [0002] In recent years, with the widespread application of Next Generation Sequence (NGS) technology, the cost of gene sequencing has dropped rapidly, and gene sequencing technology has been promoted in a wider range of fields such as biology, medicine, health, criminal investigation, agriculture, etc. application. Among them, NGS-based Whole Genome Sequencing (WGS) is a very valuable branch field that has received extensive attention. [0003] Whole genome sequencing refers to the sequencing of all the genes in the genome of a biological individual, that is, the determination of the base sequence of its deoxyribonucleic acid (Deoxyribonucleic Acid, DNA). Genomic information has been used to identify genetic diseases, find mutations that drive cancer development, and track disease outbr...

AI Technical Summary

Problems solved by technology

The disadvantage is: to achieve the same function, FPGA is generally slower than ASIC (Application Specific Integrated Circuit, ASIC), and the circuit area is larger than ASIC

However, there are two problems with the current GPU: First, due to the hardware structural characteristics of the GPU, many parallel algorithms cannot be effectively executed on the GPU; second, the GPU will generate a lot of heat during operation, and the energy consumption is high

To sum up, the above four computing devices have their own characteristics and limitations.

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