Sequencing Data Transmission via Incremental Base Extension Cycles
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Solution Overview
Problem
Current sequencing technologies face significant delays and data loss risks due to the lengthy time required to transmit large volumes of sequencing data from sequencing platforms to cloud servers, which can take over 20 hours.
Innovation Solution
A method where a sequencing system performs base extension reactions and outputs sequencing data to an external server in preset increments, allowing for simultaneous sequencing and data transmission, enabling the server to process and output base calling results promptly, thus accelerating the sequencing process and reducing data loss.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of time
If sequencing data are transmitted after the sequencing run is completed, then data transmission can be performed in batch, but the waiting time for data transmission becomes very long (over 20 hours)
Solution Approach 1:
The patent segments the large volume of sequencing data into smaller packets that can be transmitted incrementally during the sequencing run. Instead of waiting for complete sequencing data, the system transmits data packets at predetermined time intervals or when certain conditions are met, allowing parallel processing and significantly reducing the overall waiting time.
Solution Approach 2:
The patent performs preliminary data transmission during the sequencing run itself, rather than waiting for completion. By transmitting data packets in advance during the sequencing process, the system enables early processing and analysis of sequencing data, eliminating the need to wait for the entire sequencing run to finish before data transmission begins.
2Reliability
If large volumes of sequencing data are transmitted over long periods, then data can be sent in manageable batches, but the risk of data loss increases
Solution Approach 1:
By dividing sequencing data into smaller packets for transmission, the patent reduces the risk of complete data loss. If data loss occurs during transmission, only the affected packets need to be retransmitted rather than the entire dataset, thereby improving reliability while maintaining efficient transmission.
Solution Approach 2:
The patent implements error correction codes and data verification mechanisms before data transmission begins. By preparing redundancy and checksum information in advance, the system can detect and correct transmission errors without requiring retransmission, thus reducing data loss risk during the transmission process.
3Productivity
If sequencing data are transmitted in real-time during base extension cycles, then processing time is reduced, but the complexity of data management increases
Solution Approach 1:
The patent divides the sequencing data stream into manageable packets with clear delimiters and metadata. This segmentation simplifies the complexity of real-time data management by creating standardized, modular data units that can be processed independently, reducing the burden on the data management system while enabling rapid transmission.
Data Source
Figure 1
AI summary
The present application relates to the technical field of information and relates to a sequencing method. The sequencing method provided by the present application includes the following steps: using a sequencing system to perform base extension reactions on nucleic acid samples; and outputting sequencing data to an external server at nodes according to preset numbers of base extension cycles, and outputting base calling results by the external server on the basis of the sequencing data. The sequencing method provided by the present application enables the transmission of sequencing intermediate files of the preset numbers of base extension cycles and, by means of the external server, the outputting of the base calling results at nodes and thus the flexible extraction of base calling data for the sequenced samples according to preset requirements, helping increase the efficiency of sequencing of nucleic acid samples.