Software-Accelerated Genomic Read Mapping With Compact Hash Tables
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Solution Overview
Problem
Existing genomic read mapping methods are slow and require significant memory and storage resources, limiting their efficiency in processing genomic data.
Innovation Solution
A software-accelerated genomic read mapping method using a hash table indexed with genomic data signatures, encoding genomic reads into one-byte signatures and utilizing a single array hash table to reduce memory and enhance processing speed.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional genomic read mapping methods are used, then mapping accuracy can be maintained, but processing speed is slow and memory requirements are high
Solution Approach 1:
The patent extracts only the essential information from genomic reads by generating k-mer seeds and mapping them to hash table entries, discarding redundant sequence data. This extraction approach reduces memory requirements while maintaining mapping functionality through the hash table's compact structure that stores only necessary mapping information.
Solution Approach 2:
The patent creates a compressed copy of the reference genome in the form of a hash table, where only unique k-mer seeds and their corresponding positions are stored. This copy allows rapid lookup during mapping without requiring the full reference genome sequence to be loaded into memory, significantly reducing memory requirements while maintaining search accuracy.
2Productivity
If traditional genomic read mapping methods are used, then mapping completeness can be maintained, but processing time is excessive
Solution Approach 1:
The patent performs preliminary action by pre-processing the reference genome to generate and store k-mer seed mappings in a hash table before actual sequencing reads are processed. This pre-computation allows rapid lookup during the mapping process, eliminating the need for time-consuming full-reference alignment for each read, thereby significantly reducing processing time.
Solution Approach 2:
The patent replaces the mechanical system of traditional sequential alignment algorithms with a software-based hash table lookup mechanism. This substitution transforms the mapping process from computationally intensive sequential comparison to efficient O(1) hash-based retrieval, dramatically improving processing speed while maintaining mapping completeness.
Data Source
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AI summary
Methods, systems, apparatus, and computer programs are disclosed for software-accelerated genomic data read mapping. In one aspect, the method can include actions of obtaining a k-mer seed from a genomic data read, generating a genomic signature based on the obtained k-mer seed, determining a reference sequence location that match at least a portion of the k-mer seed using a hash data structure, wherein the hash data structure comprises N data cells comprising a first portion storing a predetermined genomic signature and a second portion storing a value that corresponds to a first occurrence of a reference sequence location that match at least a portion of the k-mer seed from which the predetermined genomic signature was derived, and selecting the determined reference sequence location as an actual alignment for the obtained k-mer seed based on one or more alignment scores.