Hardwired Genomic Processing Engines for Faster Sequence Analysis
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Solution Overview
Problem
Current bioinformatics methods for analyzing genomic data are labor-intensive, time-consuming, and prone to errors, particularly in building full-length genomic sequences, which hinders the efficient processing and analysis of large-scale genomic data.
Innovation Solution
Implementing a combination of software and hardware solutions, including integrated circuits with hardwired digital logic circuits, to perform bioinformatics tasks on a hardware processing platform, optimizing algorithms for faster and more accurate genetic data analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional software-based methods are used for bioinformatics analysis, then ease of operation is maintained, but productivity is low and time consumption is high
Solution Approach 1:
The patent replaces software-based processing with hardware-based processing using integrated circuits and Field-Programmable Gate Arrays (FPGAs). This substitution of mechanical/software systems with hardware systems directly addresses the contradiction by providing faster processing speeds through dedicated hardware circuits while managing complexity through programmable logic devices that can be configured for specific bioinformatics algorithms.
Solution Approach 2:
The patent divides the bioinformatics processing system into multiple parallel processing units or pipelines within the hardware architecture. By segmenting the overall processing task into concurrent operations that can be executed simultaneously across multiple hardware units, the system achieves higher productivity while distributing the complexity across modular components.
2Loss of time
If software-based methods are used, then device complexity is low, but loss of time is high
Solution Approach 1:
The patent replaces software execution with hardware implementation using FPGAs and integrated circuits. This substitution eliminates the interpretation overhead of software and executes bioinformatics algorithms directly in hardware, dramatically reducing analysis time while improving processing efficiency through parallel computation capabilities inherent in hardware architectures.
Solution Approach 2:
The patent performs preliminary configuration and setup of the hardware processing pipelines before actual data analysis begins. By pre-configuring the FPGA logic circuits and data flow paths according to specific bioinformatics protocols, the system minimizes runtime configuration overhead and ensures optimal processing speed during actual analysis, thereby reducing overall loss of time.
3Reliability
If traditional methods are used, then ease of operation is maintained, but reliability is low due to errors
Solution Approach 1:
The patent replaces software-based processing with hardware-based processing to eliminate software-related errors such as bugs, memory corruption, and execution variability. Hardware circuits provide deterministic and reproducible results, improving reliability and accuracy of bioinformatics analysis while managing hardware complexity through standardized FPGA designs and verification protocols.
Solution Approach 2:
The patent incorporates feedback mechanisms in the hardware architecture, including error detection and correction circuits, validation logic that verifies intermediate results, and quality control checkpoints throughout the processing pipeline. These feedback systems continuously monitor and correct potential errors, enhancing reliability while the modular hardware design keeps complexity manageable through systematic error handling.
Data Source
AI summary
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. The hardwired digital logic circuits are 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 sequence analysis pipeline on the reads of genomic data. In various instances, each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform one or more steps a variant call operation.