DNA Sequence Processing via Parallel Read Group Alignment
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Solution Overview
Problem
Existing DNA sequence processing methods are inefficient and lack precision in gene mutation detection due to the processing of only one sequencing library at a time, which is not optimized for multiple libraries.
Innovation Solution
A method and device for concurrently processing multiple read groups from different sequencing libraries by performing alignment computation, merging alignment results, and detecting mutations across chromosome regions, utilizing a distributed storage system and tools like BWA, Picard, and GATK to improve efficiency and precision.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If multiple sequencing libraries are processed sequentially one at a time, then the processing procedure is simple and easy to implement, but the processing efficiency is low and time-consuming
Solution Approach 1:
The patent segments the processing procedure by dividing chromosome regions into multiple partitions, allowing different read groups from multiple sequencing libraries to be processed in parallel on different computing nodes. Each partition is independently processed and then results are merged, achieving high efficiency without requiring complex coordination of the entire dataset at once.
Solution Approach 2:
The patent introduces a new dimension of parallel processing by organizing computation across multiple computing nodes and partitions simultaneously. Instead of processing libraries sequentially in one dimension, the system processes multiple libraries across multiple partitions in parallel, transforming the processing architecture from linear to multi-dimensional parallel execution.
2Measurement precision
If only one read group is processed at a time, then memory usage and computational resources are managed simply, but the detection precision for gene mutations is insufficient
Solution Approach 1:
The patent segments both the data (chromosome regions into partitions) and the processing (different read groups processed independently in parallel). This segmentation allows multiple sequencing libraries to contribute data to the same chromosome region without requiring all data to be loaded into memory simultaneously, achieving high detection precision through comprehensive data aggregation while managing resources efficiently through partitioned processing.
Solution Approach 2:
The patent introduces intermediate files as mediators that store alignment results for each partition. These intermediate files serve as temporary storage that allows results from multiple read groups to be accumulated and merged without requiring all raw data to remain in memory simultaneously, enabling precise mutation detection while controlling memory usage.
3Measurement precision
If alignment computation is performed on all reads from multiple libraries simultaneously, then comprehensive mutation detection is achieved, but the computational complexity and memory requirements increase significantly
Solution Approach 1:
The patent divides chromosome regions into multiple partitions and processes different read groups in parallel on different partitions. This segmentation allows the system to handle data from multiple sequencing libraries comprehensively for accurate mutation detection while limiting memory usage at any given time to only the data required for the current partition being processed.
Solution Approach 2:
The patent performs preliminary alignment computation for each read group separately before merging results. By pre-processing each read group independently and storing results in intermediate files, the system achieves comprehensive mutation detection capability while avoiding the memory overhead of loading all raw data from multiple libraries simultaneously into memory.
Data Source
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AI summary
A DNA sequence processing method and device are used to resolve a prior-art problem of low-efficiency mutation detection on a DNA sample. The method includes: performing the following operations on each read group concurrently: performing alignment computation on each read in the read group according to a reference sequence of a chromosome, to obtain an alignment result record of the read relative to the reference sequence; determining, according to the alignment result record, a chromosome region in which each read is located; and merging, into one intermediate result file, alignment result records of reads located in a same chromosome region, where after the foregoing operations are performed on N read group, each chromosome region is corresponding to N intermediate result files; determining a target sequence file of each chromosome region according to the N intermediate result files corresponding to the chromosome region; and determining mutation site information of each chromosome region according to the target sequence file of the chromosome region.