Genome Read Mapping Storage Using In-Memory Binary Vector Filtering
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Solution Overview
Problem
The processing of genome sequences for read mapping consumes significant computing resources and is affected by genome abnormalities, leading to inefficiencies and errors due to the manner in which subsequences of reference sequences and read sequences are stored in memory.
Innovation Solution
A storage system that includes a control unit for clustering and generating read binary vectors, a storage module for in-memory computing, and a processing device for aligning processes, utilizing techniques like Locality Sensitive Hashing and in-memory computation to improve computing efficiency and accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional read mapping processing is used where subsequences of reference sequence are stored in memory strings of bit lines and read sequences are inputted into word lines, then the processing can be completed, but computing efficiency is reduced due to the manner of storage
Solution Approach 1:
The patent inverts the traditional storage assignment by storing read sequences in bit lines and reference sequence subsequences in word lines, opposite to the conventional approach. This inversion enables more efficient computing operations during read mapping, improving productivity while managing device complexity
Solution Approach 2:
The patent changes the storage parameters and data organization format to optimize computing efficiency. By modifying how sequences are stored and assigned to memory lines, the system achieves faster processing without proportionally increasing device complexity
2Measurement precision
If genome sequences are processed for read mapping, then mapping results can be obtained, but a large amount of computing resources are consumed due to the long lengths of genome sequences
Solution Approach 1:
The patent segments the genome sequences into smaller subsequences and organizes them in a clustered format. This segmentation allows the processing system to handle large genome sequences in manageable portions, reducing overall computing resource consumption while maintaining mapping accuracy through systematic processing of segmented data
Solution Approach 2:
The patent performs preliminary clustering and organizing of read sequences before the main mapping process. By pre-processing and grouping similar sequences together, the system reduces the computational burden during the actual mapping operation, thereby reducing energy consumption while preserving mapping precision
3Reliability
If traditional storage and processing methods are used, then read mapping can be performed, but operating errors may be caused by genome abnormalities in the sequences
Solution Approach 1:
The patent implements a feedback mechanism where read sequences are clustered and compared systematically. This feedback loop allows the system to identify and handle genome abnormalities more effectively, improving mapping reliability by detecting and correcting errors through iterative comparison and clustering validation
Solution Approach 2:
The patent changes processing parameters through clustering and reorganizing sequence data in a way that highlights abnormalities. By transforming the data organization and processing approach, the system improves reliability in detecting genome abnormalities without excessively increasing processing complexity
Data Source
AI summary
A storage system capable of executing data processing, includes the following elements. A first control unit of a storage device, for cooperating with a sequencer to perform a clustering process on a plurality of original sequences to obtain a plurality of read sequences, generating a plurality of read binary vectors corresponding to the read sequences, and generating a pruned filtering binary vector according to a reference sequence. A first storage module of the storage device, for storing the read binary vectors and the pruned filtering binary vector, and executing an in-memory computing (IMC) according to the read binary vectors and the pruned filtering binary vector, so as to generate a filtered cluster read set. A processing device, for executing an aligning process according to the filtered cluster read set and the reference sequence.