Incremental Sequence Alignment for Parallel Nucleic Acid Analysis
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Solution Overview
Problem
Conventional nucleic acid sequencers face inefficiencies due to the lack of computational resources to perform primary and secondary analysis operations in parallel, leading to prolonged downtime and reduced throughput, which affects the processing time and reagent consumption.
Innovation Solution
Offloading secondary analysis operations to a programmable logic unit with hardwired digital logic, allowing for parallel execution of sequencing and secondary analysis operations, such as mapping and aligning, using hardware circuits.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional nucleic acid sequencers perform primary and secondary analysis operations sequentially using general-purpose processors, then computational flexibility is maintained, but processing time increases and throughput decreases
Solution Approach 1:
The system segments the analysis workflow into distinct functional units (mapping unit, alignment unit, variant calling unit) that can operate independently and in parallel. Each unit is implemented as a separate hardware module with dedicated digital logic circuits, allowing simultaneous execution of multiple analysis operations on different data sets without resource conflicts.
Solution Approach 2:
The patent replaces general-purpose software-based processing with hardware-based digital logic circuits. Mapping, alignment, and variant calling operations are implemented using combinatorial logic and sequential logic circuits that execute operations in parallel at clock speeds significantly faster than software execution, thereby reducing processing time and increasing throughput.
2Speed
If computational resources are dedicated to secondary analysis operations, then analysis speed improves, but available resources for sequencing operations decrease
Solution Approach 1:
The system architecture divides computational resources into separate hardware modules for sequencing operations and secondary analysis operations. The mapping unit, alignment unit, and variant calling unit are implemented as independent hardware circuits that can process data simultaneously with the sequencing device, eliminating resource contention and enabling parallel execution of sequencing and analysis tasks.
Solution Approach 2:
The hardware-based secondary analysis units begin processing sequencing data immediately as it becomes available, rather than waiting for complete sequencing runs. The mapping unit starts mapping reads to the reference genome during ongoing sequencing, and the alignment unit begins alignment operations on mapped data in real-time, thereby accelerating analysis speed without impacting sequencing throughput.
3Productivity
If parallel execution of sequencing and secondary analysis is implemented using hardware circuits, then processing time reduces and throughput increases, but device complexity increases
Solution Approach 1:
The system is divided into modular hardware units (mapping unit with mapping circuit, alignment unit with alignment circuit, variant calling unit with variant calling circuit), each implementing specific functions with dedicated digital logic. This modular architecture manages complexity by localizing functions to discrete modules while enabling parallel operation, thereby achieving high throughput without unmanageable system complexity.
Data Source
AI summary
Methods, systems, and apparatuses, including computer programs, for performing incremental secondary analysis of nucleic acid sequence reads. The method can include (i) obtaining first data describing a plurality of first reads generated by a nucleic acid sequencing device during a first read interval, (ii) obtaining second data describing a plurality of second reads generated by the nucleic acid sequencing device during a second read interval that is performed after the first read interval, wherein while the second data is being obtained: (a) providing, by the nucleic acid sequencing device, the first data as an input to a mapping and alignment unit, (b) receiving, from the mapping and alignment unit, alignment results, and (c) storing the received alignment results, and, thereafter (iii) instructing the mapping and alignment unit to begin alignment of the second data representing the second plurality of reads to the reference sequence.