Integrated Circuit Genomic Pipeline for Fast Sequence Alignment
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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 needed for personalized healthcare.
Innovation Solution
Implementing bioinformatics protocols on an integrated circuit processing platform using hardware accelerators with hardwired digital logic circuits, configured as processing engines, to perform tasks such as sequence analysis, mapping, alignment, and sorting, thereby optimizing the processing of genomic data for faster and more accurate results.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional software-based bioinformatics methods are used for genomic data analysis, then flexibility and adaptability are maintained, but processing time is excessive and productivity is low
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 sequence analysis, mapping, and alignment operations in parallel, transforming the mechanical software execution into hardware-level operations that execute simultaneously across multiple processing engines.
Solution Approach 2:
The patent divides the genomic data processing task into multiple independent processing engines, each capable of handling specific operations such as k-mer counting, sequence mapping, or alignment. These segmented processing units operate in parallel on different portions of the genomic data, collectively achieving full-length sequence assembly much faster than sequential software processing.
2Reliability
If manual or software-based methods are used for building full-length genomic sequences, then accuracy can be maintained through careful processing, but the process is labor-intensive and time-consuming
Solution Approach 1:
The patent replaces manual and software-based sequence assembly with hardware-based assembly using dedicated processing engines that perform error-corrected k-mer counting and consensus sequence generation. The hardware implementation maintains accuracy through multiple verification steps while eliminating human error and reducing processing time significantly.
Solution Approach 2:
The patent uses multiple copies of processing engines that simultaneously analyze the same genomic data from different perspectives. Each engine independently processes the data and generates results that are then compared and reconciled, ensuring high accuracy through redundancy while distributing the computational complexity across multiple identical units.
3Productivity
If hardware accelerators with hardwired logic circuits are implemented, then processing speed and productivity are significantly improved, but device complexity increases
Solution Approach 1:
The patent designs processing engines that can perform multiple bioinformatics operations through configuration rather than dedicated hardware for each function. The same hardware platform can be reconfigured to perform different tasks such as mapping, alignment, variant calling, or assembly, reducing overall device complexity while maintaining high productivity across diverse genomic analysis applications.
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. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. 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. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.