Method for computing chromosome copy number based on hardware-software collaboration

By employing a hardware-software co-computation approach, and utilizing FPGA for parallel computing and bitwise operations to optimize edit distance, the problem of low computational performance in traditional methods is solved, achieving efficient chromosome copy number calculation.

CN117275573BActive Publication Date: 2025-12-12NANJING GEZHI GEMONICS CO LTD
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Patent Information

Application Number
CN202311380149.2
Authority / Receiving Office
CN · China
Patent Type
Patents(China)
Current Assignee / Owner
Filing Date
2023-10-24
Publication Date
2025-12-12
Estimated Expiration
2043-10-24

AI Technical Summary

Technical Problem

In the existing technology, traditional motif data processing methods have low computer performance and energy efficiency ratio when processing chromosome copy number calculations, and the computing performance is limited, resulting in long calculation time and serious waste of resources.

Method used

A hardware-software co-computation approach is adopted, utilizing FPGA for parallel computing and bitwise operations to optimize distance calculation, and combining it with CPU for result processing, thereby shortening the calculation steps and reducing hard disk I/O operations.

Benefits of technology

It significantly improves the performance and energy efficiency of chromosome copy number calculation, shortens processing time, reduces resource waste, and improves computational efficiency.

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Abstract

The present application relates to the technical field of gene sequencing data processing, and particularly relates to a method for calculating chromosome copy number based on software and hardware cooperation, comprising the following steps: S1, separately forming an odd item or an even item of a reference genome sequence R into a subset Rc; S2, indexing the subset Rc through a hash function; S3, mapping a sequencing sequence obtained by gene sequencing back to a position of the reference genome; S4, extracting a seed set So of the subset Qo, finding all candidate positions Lp in an index table SI, and determining an exact position of Q mapping to R; and S5, after completing all sequencing data processing, counting the number of sequencing sequences in each block, and performing normalization. The present application innovatively reduces a standard three-step calculation process completed by three independent programs into a one-step method, that is, a program directly outputs a result without additional hard disk IO reading and writing, thereby shortening the calculation steps.
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Citation Information

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