Integrated Circuit Genomics Pipeline With FPGA Hardware Acceleration
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Solution Overview
Problem
Current bioinformatics systems face challenges in efficiently processing large volumes of genomic data from Next Gen Sequencers, requiring significant computational resources and incurring high costs, while existing software solutions are labor-intensive and prone to errors.
Innovation Solution
A hybrid CPU and FPGA platform is employed for executing bioinformatics protocols, featuring integrated circuits with hardwired digital logic circuits that perform tasks such as mapping, alignment, and variant calling, optimizing processing speed and accuracy through hardware acceleration.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If software-based bioinformatics tools are used to process genomic data, then processing accuracy can be maintained, but processing speed becomes extremely slow and computational costs increase significantly
Solution Approach 1:
The patent replaces software-based processing with hardware-based processing using FPGAs and ASICs. The bioinformatics algorithms are implemented as hardwired digital logic circuits that perform mapping, alignment, and variant calling operations in parallel, achieving orders of magnitude speedup while maintaining processing accuracy through deterministic hardware execution
Solution Approach 2:
The patent divides the bioinformatics processing pipeline into distinct modular stages including quality control, mapping, alignment, and variant calling. Each stage is implemented as a separate hardware module that can process data independently and in parallel, improving overall processing throughput while maintaining accuracy at each stage
2Productivity
If more computational resources are allocated to process genomic data, then processing capacity increases, but system complexity and operational costs increase
Solution Approach 1:
The patent employs dynamically reconfigurable FPGA architectures that can adapt their internal logic structure based on the specific bioinformatics algorithm being executed. This allows the same hardware platform to handle different processing tasks with varying resource requirements, optimizing processing capacity while managing system complexity through flexible resource allocation
Solution Approach 2:
The patent creates a universal hardware platform that can execute multiple different bioinformatics algorithms and processing pipelines. The FPGA and ASIC designs incorporate configurable logic blocks and reusable computational units that can be programmed to perform mapping, alignment, sorting, and variant calling operations, eliminating the need for separate dedicated systems for each function
Data Source
AI summary
A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.