Methods, apparatus, equipment and storage media for filtering gene sequencing signals

Abstract

A method, apparatus, device, and storage medium for filtering gene sequencing signals are disclosed. The method includes: obtaining multiple sets of raw gene sequencing signals based on current changes generated by different bases passing through nanopores; in a first-stage pipeline, filtering each set of raw gene sequencing signals at the current time point to obtain preliminary gene sequencing signals; in a second-stage pipeline, storing the preliminary gene sequencing signals in a preset register and filtering the raw gene sequencing signals at the next time point to obtain candidate gene sequencing signals; and in a third-stage pipeline, storing the candidate gene sequencing signals in the register and outputting the preliminary gene sequencing signals to a host computer. This method can improve the filtering efficiency of gene sequencing signals.

Description

Method, device, equipment and storage medium for filtering gene sequencing signals Technical Field

[0001] The present application relates to the field of biotechnology, and in particular to a method and apparatus for filtering and processing gene sequencing signals, a device, and a storage medium. Background Art

[0002] Nanopore sequencing, an emerging high-throughput sequencing technology, offers advantages such as single-molecule sequencing and real-time sequencing. It enables efficient processing and analysis of gene sequencing signals. However, the gene sequencing signals acquired by nanopore sequencing are affected by factors such as noise during the acquisition and transmission process, resulting in glitches. These glitches can affect subsequent analysis and research of the gene sequencing signals. Therefore, filtering of the gene sequencing signals is necessary.

[0003] Related technologies use software to filter and process gene sequencing signals one by one before storing them in registers. However, the sheer number of gene sequencing signals requires significant bandwidth and storage resources to process them individually, resulting in inefficient processing. Therefore, improving the efficiency and speed of gene sequencing signal filtering has become a pressing technical challenge.

[0004] Summary of the Invention

[0005] The main purpose of the embodiments of the present application is to provide a filtering processing method and device, equipment and storage medium for gene sequencing signals, aiming to improve the filtering efficiency of gene sequencing signals.

[0006] To achieve the above objectives, a first aspect of an embodiment of the present application provides a method for filtering gene sequencing signals, the method comprising:

[0007] Based on the current changes generated by different bases passing through the nanopore, multiple sets of original gene sequencing signals are obtained;

[0008] In the first stage pipeline, each set of the original gene sequencing signals at the current time point is filtered to obtain a preliminary gene sequencing signal;

[0009] In the second-stage pipeline, the preliminary gene sequencing signal is stored in a preset register, and the original gene sequencing signal at the next time point is filtered to obtain a candidate gene sequencing signal; wherein the next time point is the time point after the current time point;

[0010] In the third stage pipeline, the candidate gene sequencing signal is stored in the register, and the preliminary gene sequencing signal is output to the host computer.

[0011] In some embodiments, filtering each set of the raw gene sequencing signals at the current time point to obtain a preliminary gene sequencing signal includes:

[0012] Performing offset processing on each group of the original gene sequencing signals at the current time point through a normalization module to obtain multiple first gene sequencing signals;

[0013] Performing filtering processing on the plurality of first gene sequencing signals through a target filter module to obtain a second gene sequencing signal;

[0014] The second gene sequencing signal is subjected to offset and truncation processing by a data offset module to obtain the preliminary gene sequencing signal.

[0015] In some embodiments, filtering the plurality of first gene sequencing signals using a target filter module to obtain a second gene sequencing signal includes:

[0016] Performing product processing on each of the first gene sequencing signals using the target filter module and a preset tap coefficient to obtain a fourth gene sequencing signal;

[0017] The target filter module calculates the sum of the plurality of fourth gene sequencing signals to obtain the second gene sequencing signal.

[0018] In some embodiments, before filtering the plurality of first gene sequencing signals using a target filter module to obtain a second gene sequencing signal, the method further includes:

[0019] Obtaining filtering requirement information of the original gene sequencing signal;

[0020] Filtering target filtering configuration parameters from preset candidate filtering configuration parameters according to the filtering requirement information;

[0021] The preset original filter module is configured according to the target filter configuration parameters to obtain the target filter module.

[0022] In some embodiments, the target filter configuration parameters include: preset tap coefficients, preset parameter quantity and preset point number information; the preset original filter module is configured according to the target filter configuration parameters to obtain the target filter module, including

[0023] Setting a preset response frequency of the original filter module according to the preset tap coefficient to obtain a target response frequency;

[0024] Setting the order of the original filter module according to the preset number of parameters to obtain a target order;

[0025] Setting the dynamic range of the original filter module according to the preset number of points to obtain a target dynamic range;

[0026] The original filter module is configured according to the target response frequency, the target order and the target dynamic range to obtain a target filter module.

[0027] In some embodiments, the raw gene sequencing signals are output by a quantization circuit, and the quantization circuit includes: a sampling module and an analog-to-digital conversion module; the multiple sets of raw gene sequencing signals are obtained based on the current changes generated by different bases passing through the nanopore, including:

[0028] The sampling module collects the current changes generated by different bases passing through the nanopore to obtain multiple groups of target current simulation signals;

[0029] The analog-to-digital conversion module performs analog-to-digital conversion on the multiple sets of target current analog signals to obtain multiple sets of original gene sequencing signals.

[0030] In some embodiments, the sampling module includes: a switch unit, an integrating amplifier, and a sample-and-hold device; the sampling module collects current changes generated by different bases passing through the nanopore to obtain multiple sets of target current analog signals, including:

[0031] The switching unit collects the current changes generated by different bases passing through the nanopore to obtain multiple groups of preliminary current simulation signals;

[0032] amplifying each of the preliminary current analog signals by the integrating amplifier to obtain a candidate current analog signal;

[0033] The candidate current analog signals are held by the sample and hold device to obtain multiple groups of target current analog signals.

[0034] To achieve the above-mentioned objectives, a second aspect of the embodiments of the present application provides a filtering processing device for gene sequencing signals, which is applied to the filtering processing device for gene sequencing signals described in the first aspect. The device includes:

[0035] A quantization circuit is used to collect the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current simulation signals;

[0036] an analog-to-digital conversion module, electrically connected to the quantization circuit, for performing analog-to-digital conversion on the target current analog signal to obtain multiple sets of original gene sequencing signals;

[0037] a target filter module, electrically connected to the analog-to-digital conversion module, for filtering the original gene sequencing signal to obtain a target gene sequencing signal;

[0038] The host computer is communicatively connected to the target filter module and is used to receive the target gene sequencing signal.

[0039] To achieve the above-mentioned purpose, the third aspect of an embodiment of the present application proposes a computer device, which includes a memory and a processor, wherein the memory stores a computer program, and the processor implements the method described in the first aspect when executing the computer program.

[0040] To achieve the above-mentioned purpose, the fourth aspect of the embodiments of the present application proposes a computer-readable storage medium, which stores a computer program. When the computer program is executed by a processor, it implements the method described in the first aspect.

[0041] The filtering processing method, device, equipment, and storage medium for gene sequencing signals proposed in this application obtain multiple sets of original gene sequencing signals. When filtering, the first-stage pipeline processes the multiple sets of original gene sequencing signals in parallel. After the filtered gene sequencing signals are stored in a register in the second-stage pipeline, the gene sequencing signals at the next time point are filtered simultaneously. In the third-stage pipeline, the gene sequencing signals stored in the second-stage pipeline are output to the host computer to achieve pipeline filtering processing, improve the speed and efficiency of gene sequencing signal filtering processing, and thus improve the overall performance of the system. BRIEF DESCRIPTION OF THE DRAWINGS

[0042] FIG1 is a flow chart of a method for filtering gene sequencing signals provided in an embodiment of the present application;

[0043] FIG2 is a schematic diagram of the structure of a quantization circuit in an embodiment of the present application;

[0044] FIG3 is a schematic structural diagram of an FIR filter circuit in an embodiment of the present application;

[0045] FIG4 is a schematic structural diagram of a target filter module in an embodiment of the present application;

[0046] FIG5 is a schematic diagram of a filtering process in a filtering method for gene sequencing signals provided in an embodiment of the present application;

[0047] FIG6 is a timing diagram of filtering processing in the related art;

[0048] FIG7 is a timing diagram of a filtering processing method for gene sequencing signals provided in an embodiment of the present application;

[0049] FIG8 is an overall flow chart of a filtering processing method for gene sequencing signals provided in an embodiment of the present application;

[0050] FIG9 is a schematic structural diagram of a filtering and processing device for gene sequencing signals provided in an embodiment of the present application;

[0051] FIG10 is a schematic diagram of the hardware structure of a computer device provided in an embodiment of the present application. DETAILED DESCRIPTION

[0052] In order to make the purpose, technical solutions and advantages of this application more clear, the following further describes this application in detail with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are only used to explain this application and are not intended to limit this application.

[0053] It should be noted that although the device schematics illustrate functional module divisions and the flowcharts illustrate logical sequences, in certain circumstances, the steps shown or described may be performed in a sequence that differs from the module divisions in the device or the sequence in the flowcharts. The terms "first," "second," and so on, in the specification, claims, and drawings, are used to distinguish similar items and are not necessarily used to describe a specific sequence or precedence.

[0054] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which this application pertains. The terms used herein are for the purpose of describing the embodiments of this application only and are not intended to limit this application.

[0055] First, let’s analyze some of the terms used in this application:

[0056] Gene sequencing signal: data obtained through various technical means during the gene sequencing process. These data can reflect the sequence information of the DNA or RNA to be sequenced.

[0057] Bases are essential building blocks of nucleic acids (DNA and RNA). They combine with sugars and phosphates to form nucleotides, the chemical basis of genetic information. Bases can be divided into two main groups: purines and pyrimidines.

[0058] Nanopore sequencing is an emerging third-generation sequencing technology that identifies nucleic acid sequences by detecting changes in the electrical signal generated when a single molecule passes through a nanopore. This technology offers advantages such as real-time, long read lengths, and the absence of PCR amplification, providing a new tool for genomic research. However, the processing and analysis of nanopore sequencing signals present challenges, requiring the use of sophisticated signal processing techniques to improve data accuracy and reliability.

[0059] Finite impulse response (FIR) filters are a key concept in digital signal processing, widely used in fields such as audio processing, image processing, and communication systems. A FIR filter's characteristic is that its system function depends only on the current input and a certain number of past inputs, not on past outputs. This gives FIR filters stability and linear phase characteristics, making them ideal for applications requiring strict phase control.

[0060] User Datagram Protocol (UDP): A simple, datagram-oriented transport layer protocol. Compared to the Transmission Control Protocol (TCP), UDP does not provide reliability guarantees and does not perform connection establishment, maintenance, or termination. This means it does not guarantee the order or integrity of data packets, nor the timing relationships between packets. Precisely because of its simplicity, UDP is widely used in situations requiring low latency and high efficiency, such as video and audio streaming, online gaming, and certain real-time communication systems.

[0061] Three-stage pipelining is a common concept in computer architecture, particularly CPU design, used to improve processor efficiency and execution speed. Pipelining technology achieves this by breaking down the instruction execution process into several stages and enabling these stages to be processed in parallel, thereby increasing processing speed. Three-stage pipelining means that the entire instruction execution process is divided into three basic stages.

[0062] Gene sequencing signals are a crucial data type in biological research, recording the genetic information within an organism. However, due to factors such as noise during acquisition and transmission, these signals often contain glitches, which can interfere with subsequent analysis and research. Therefore, glitches in gene sequencing signals need to be processed to improve their quality and accuracy.

[0063] In the related art, Python's software filtering method is used to remove noise and glitch signals from gene sequencing signals, and the software filtering method includes techniques such as median filtering, smoothing filtering, and bandpass filtering to remove noise and glitch signals and improve gene sequencing signals. However, the problem with using software filtering methods is that, because the filtering process includes filtering steps, storing in registers, and outputting to the host computer, if one gene sequencing signal is filtered and stored before processing the next gene sequencing signal, due to the large and complex number of gene sequencing signals, a large amount of transmission bandwidth and storage resources may be required, resulting in low efficiency. In addition, data preprocessing, load calculation algorithms, and feature selection will increase the computational burden, resulting in excessive time, affecting the timeliness and practicality of the analysis.

[0064] Based on this, the embodiments of the present application provide a filtering processing method and device, equipment and storage medium for gene sequencing signals, which aims to obtain multiple groups of original gene sequencing signals, first filter the multiple groups of original gene sequencing signals in parallel, and after storing the filtered gene sequencing signals in a register, simultaneously filter the gene sequencing signals at the next time point, thereby realizing pipeline filtering processing, improving the filtering processing speed and efficiency of the gene sequencing signals, and thus improving the overall performance of the system.

[0065] The filtering processing method, device, equipment and storage medium for gene sequencing signals provided in the embodiments of the present application are specifically illustrated through the following embodiments. First, the filtering processing method for gene sequencing signals in the embodiments of the present application is described.

[0066] The embodiments of the present application can acquire and process relevant data based on artificial intelligence technology. Artificial Intelligence (AI) is the theory, method, technology, and application system that uses digital computers or machines controlled by digital computers to simulate, extend, and expand human intelligence, perceive the environment, acquire knowledge, and use knowledge to achieve optimal results.

[0067] Fundamental AI technologies generally include sensors, dedicated AI chips, cloud computing, distributed storage, big data processing, operating / interaction systems, and mechatronics. AI software technologies primarily encompass computer vision, robotics, biometrics, speech processing, natural language processing, and machine learning / deep learning.

[0068] The filtering processing method of the gene sequencing signal provided in the embodiment of the present application relates to the field of artificial intelligence technology. The filtering processing method of the gene sequencing signal provided in the embodiment of the present application can be applied to the terminal, can also be applied to the server side, and can also be software running in the terminal or the server side. In some embodiments, the terminal can be a smart phone, a tablet computer, a laptop computer, a desktop computer, etc.; the server side can be configured as an independent physical server, or can be configured as a server cluster or distributed system composed of multiple physical servers, and can also be configured as a cloud server that provides basic cloud computing services such as cloud services, cloud databases, cloud computing, cloud functions, cloud storage, network services, cloud communications, middleware services, domain name services, security services, CDN, and big data and artificial intelligence platforms; the software can be an application of the filtering processing method for gene sequencing signals, etc., but is not limited to the above forms.

[0069] The present application can be used in many general or special computer system environments or configurations. For example: personal computers, server computers, handheld or portable devices, tablet devices, multiprocessor systems, microprocessor-based systems, set-top boxes, programmable consumer computer devices, network PCs, minicomputers, mainframe computers, distributed computing environments including any of the above systems or devices, etc. The present application can be described in the general context of computer-executable instructions executed by a computer, such as program modules. Generally, program modules include routines, programs, objects, components, data structures, etc. that perform specific tasks or implement specific abstract data types. The present application can also be practiced in distributed computing environments, in which tasks are performed by remote processing devices connected via a communication network. In a distributed computing environment, program modules can be located in local and remote computer storage media including storage devices.

[0070] FIG1 is an optional flowchart of a filtering processing method for gene sequencing signals provided in an embodiment of the present application. The method in FIG1 may include but is not limited to steps S101 to S104.

[0071] Step S101 : obtaining multiple sets of original gene sequencing signals based on the current changes generated by different bases passing through the nanopore.

[0072] It's important to note that nanopore sequencing technology works by detecting the components of individual nucleic acids. Passing different bases through a nanopore generates a change in current, which is then collected to generate a raw sequencing signal. Specifically, raw sequencing signals are collected at preset intervals. Multiple current change signals collected at intervals are converted into raw sequencing signals, resulting in a continuous generation of raw sequencing signals.

[0073] In some embodiments, the raw gene sequencing signal is a digital signal, but the current signal is an analog signal. Therefore, the current signal generated by the bases passing through the nanopore, collected by the quantization circuit, needs to be converted into a digital signal. It should be noted that the quantization circuit represents the current signal generated by digital quantization.

[0074] That is, in some embodiments, obtaining multiple sets of raw gene sequencing signals based on the current changes generated by different bases passing through the nanopore may include:

[0075] The sampling module collects the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current simulation signals;

[0076] Multiple sets of target current analog signals are converted into digital signals through the analog-to-digital conversion module to obtain multiple sets of original gene sequencing signals.

[0077] The sampling module is connected to a single-molecule nanopore sequencing device, which allows only one base molecule to pass through the nanopore at a time. Each base's passage through the nanopore causes a slight current change, which is collected by the sampling module and pre-processed to generate multiple sets of target current simulation signals.

[0078] It should be noted that preprocessing includes amplification and sample-and-hold processing. Because weak current changes make it difficult to distinguish different bases, and therefore difficult to analyze the composition of nucleic acids, amplification generates a target current analog signal that makes it easier to distinguish different bases. Sample-and-hold processing is a crucial step in analog signal processing. Because the current change generated by a base passing through the nanopore is an instantaneous value, this value must be maintained for a period of time to subsequently generate the target current analog signal.

[0079] That is, in some embodiments, the sampling module collects the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current simulation signals, which may include:

[0080] The switching unit collects the current changes generated by different bases passing through the nanopore to obtain multiple sets of preliminary current simulation signals;

[0081] amplifying each preliminary current analog signal through an integrating amplifier to obtain a candidate current analog signal;

[0082] The candidate current analog signals are held by a sample-and-hold device to obtain multiple groups of target current analog signals.

[0083] It should be noted that, as shown in Figure 2, the quantization circuit includes a switch unit, an integrating amplifier, a sample holder and an analog-to-digital conversion module, and the sampling module includes a switch unit, an integrating amplifier and a sample holder. The input end of the switch unit is connected to the nanopore sequencing device, the output end of the switch unit is connected to the input end of the integrating amplifier, the output end of the integrating amplifier is connected to the input end of the sample holder, and the output end of the sample holder is connected to the input end of the analog-to-digital conversion module.

[0084] The current change signal output by the nanopore sequencing device is first input through the switching unit to obtain a preliminary current simulation signal. It should be noted that the preliminary current simulation signal is the current change signal collected directly from the nanopore sequencing device, so glitches may exist during the collection and transmission process and need to be filtered out.

[0085] Specifically, the switch unit is a sensor array, which captures the current change signal output by the nanopore sequencing device through the sensor array to obtain a preliminary current simulation signal.

[0086] It should be noted that the current change caused by the bases passing through the nanopore is weak, so the preliminary current analog signal is amplified to highlight the current differences between different bases. Specifically, this embodiment uses an integrating amplifier to amplify the preliminary current analog signal and performs an integral operation on the preliminary current analog signal to obtain a candidate current analog signal.

[0087] Specifically, because the switch unit captures the current changes generated by the bases passing through the nanopore over a very short period of time, the candidate current analog signal is an instantaneous value. This signal must be held for a period of time before filtering can be performed. Therefore, in this embodiment, a sample-and-hold device is used to hold the candidate current analog signal for a period of time to obtain the target current analog signal.

[0088] It should be noted that the target current analog signal is output to the analog-to-digital conversion module, so that the analog-to-digital conversion module converts the target current analog signal into an original gene sequencing signal of a digital signal.

[0089] After the processed target current analog signal is completed, it is necessary to convert the target current analog signal into the original gene sequencing signal. First, the original gene sequencing signal at the current time point is input into multiple registers in parallel, and then read out from the multiple registers in parallel and input into the filter circuit, and filtered through the filter circuit.

[0090] Step S102 : In the first stage pipeline, each set of original gene sequencing signals at the current time point is filtered to obtain a preliminary gene sequencing signal.

[0091] It should be noted that each set of raw gene sequencing signals contains multiple signals, and the number of raw gene sequencing signals in each set is the same. In this embodiment, each set contains 8 raw gene sequencing signals, and 16 registers are configured to perform filtering processing on each set of raw gene sequencing signals in parallel, thereby improving the speed and efficiency of filtering the raw gene sequencing signals. It should be noted that other embodiments can set the number of registers as needed, and this embodiment does not impose a specific limit on the number of registers.

[0092] Specifically, the original gene sequencing signal at the current point in time is the current change signal generated by different bases passing through the nanopore during the previous preset time period. It should be noted that when processing the current change generated by the nanopore to obtain the original gene sequencing signal, the use of an FIR filter circuit in this embodiment is a common choice, and other embodiments can use an IIR filter circuit. It should be emphasized that the choice of an FIR filter circuit or an IIR filter circuit depends on the actual scenario requirements, that is, the selection of an FIR filter circuit or an IIR filter circuit is determined based on linear phase requirement information, compact design requirement information, or other filtering requirements.

[0093] Among them, the FIR filter circuit has a linear phase characteristic, which is very important for maintaining the phase information of the original gene sequencing signal, especially when designing accurate signal analysis and interpretation. In addition, the FIR filter circuit is stable and will not cause unstable oscillations or singularities, which enhances the stability of the original gene sequencing signal processing and maintains the quality and reliability of the original gene sequencing signal. It should be emphasized that the FIR filter circuit allows precise control of the frequency response of the filter, including the cutoff frequency, passband and stopband characteristics, to meet the specific requirements of the original gene sequencing signal processing. In addition, the FIR filter circuit is simple in hardware implementation because the FIR filter circuit does not involve a recursive structure, but a direct weighted summation operation, which is more suitable for real-time or highly generated original gene sequencing signal processing. Therefore, this embodiment uses an FIR filter circuit to filter the original gene sequencing signal.

[0094] That is, in some embodiments, filtering each set of original gene sequencing signals at the current time point to obtain preliminary gene sequencing signals may include:

[0095] Performing offset processing on each set of original gene sequencing signals at the current time point through a normalization module to obtain multiple first gene sequencing signals;

[0096] Performing filtering processing on the plurality of first gene sequencing signals through a target filter module to obtain a second gene sequencing signal;

[0097] The second gene sequencing signal is offset and truncated by the data offset module to obtain a preliminary gene sequencing signal.

[0098] It's important to note that to improve the quality and accuracy of the raw gene sequencing signal, an additional filtering step is required. Therefore, several modules have been added to the FIR filter circuit to enhance the quality and accuracy of filtering. As shown in Figure 3, the FIR filter circuit includes a normalization module, a target filter module, and a data offset module. The normalization module offsets the raw gene sequencing signal after conversion by the analog-to-digital conversion module to improve filtering accuracy. The target filter module performs filtering, while the data offset module offsets and truncates the filtered signal. The offset and truncation steps maintain signal accuracy while preparing the subsequent signal output to the host computer for subsequent processing.

[0099] The normalization module is used to adjust the signal distribution. In this embodiment, the raw gene sequencing signal obtained using nanopore sequencing technology is unique and falls within a specific range. Using the normalization module to offset the raw gene sequencing signal ensures that valid data falls within the passband of the target filter module, helping to optimize the filtering effect.

[0100] It should be noted that the target filter module performs filtering processing, that is, extracts the original gene sequencing signal according to the preset frequency. Specifically, in nanopore sequencing, the digital domain is theoretically extracted at 1 times, but before extraction, the spectrum of the original gene sequencing signal will be expanded by 1 times. In order to avoid confusion problems, it is necessary to limit the frequency of the original gene sequencing signal before extraction to within the range of ±π / 2. However, the actual target filter module needs to set a transition zone, and the design is based on ±π / 4 to adapt to the transition zone. Therefore, before the target filter module performs filtering, the frequency of the original gene sequencing signal before extraction is limited to ±π / 4.

[0101] Specifically, the transition zone is narrow, and a narrow transition zone requires a higher filter order, which increases hardware costs. To address this, a data offset module is added to the target filter module, eliminating the need for a higher filter order. The data offset module further offsets and truncates the second gene sequencing signal output by the target filter to obtain a preliminary gene sequencing signal, resulting in an accurate and clean gene sequencing signal.

[0102] In some embodiments, the target filter module is a filter module suitable for current filtering processing, so the original filter needs to be configured as the target filter in advance, and the configuration process of the target filter includes:

[0103] Obtain filtering requirement information for raw gene sequencing signals;

[0104] Filtering target filter configuration parameters from preset candidate filter configuration parameters according to the filter requirement information;

[0105] The preset original filter module is configured according to the target filter configuration parameters to obtain the target filter module.

[0106] It should be noted that the filtering processing of different original gene sequencing signals requires the configuration of different target filter modules to meet the requirements of filtering processing of different original gene sequencing signals.

[0107] Among them, the filtering requirement information represents the demand for filtering the original gene sequencing signal. It should be noted that the filtering requirement signal is determined according to the noise characteristics in the original gene sequencing signal, and the demand for filtering the original gene sequencing signal includes any one of the following: response frequency requirement, performance requirement, accuracy requirement and dynamic range requirement. Among them, the response frequency requirement represents the signal of which frequency band the target filter module needs to respond, the performance requirement represents the performance requirements for the target filter module, the accuracy requirement represents the filtering accuracy of the target filter module, and the dynamic range requirement represents the error range allowed by the target filter module. Therefore, the corresponding target filter configuration parameters are screened out from multiple candidate filter configuration parameters according to the filtering requirement information, and the target filter configuration parameters can meet the filtering requirement signal.

[0108] In some embodiments, the original filter module is configured according to the target filter configuration parameters to construct a target filter module that meets the filtering requirements. Therefore, pre-configuring the original filter module allows the filter module to be flexibly configured according to requirements to achieve the specified filtering effect. Therefore, in this embodiment, the filter module is configured in advance to generate a target filter module to meet the filtering requirements of different original gene sequencing signals.

[0109] It should be noted that the filtering requirement information includes: response frequency requirements, performance requirements, accuracy requirements and dynamic range requirements, so the target filtering configuration parameters include: preset tap coefficients, preset parameter numbers and preset point information. The preset tap coefficients are the coefficients of each level of the target filter module, and the preset tap coefficients can set the filter's processing method for the original gene sequencing signal. The preset tap coefficients in this embodiment are used to set the response frequency of the filter, and other embodiments can be set to amplify or attenuate signals of different frequencies. The preset parameter number is used to set the order of the filter to meet performance requirements, and the preset point information is used to set the accuracy and dynamic range of the filter to meet accuracy requirements and dynamic range requirements.

[0110] That is, in some embodiments, configuring the preset original filter module according to the target filtering configuration parameters to obtain the target filter module specifically includes:

[0111] Setting the response frequency of the preset original filter module according to the preset tap coefficient to obtain the target response frequency;

[0112] The order of the original filter module is set according to the preset number of parameters to obtain the target order;

[0113] The dynamic range of the original filter module is set according to the preset number of points to obtain the target dynamic range;

[0114] The original filter module is configured according to the target response frequency, target order and target dynamic range to obtain a target filter module.

[0115] It should be noted that, as shown in Figure 4, the target filter module of this embodiment includes a control module, a convolution operation module, and a normalization module. Among them, the control module is used to receive filtering requirement information from the host computer, select target filtering configuration parameters based on the filtering requirement information, and configure the original filter based on the target filtering configuration parameters, and the target filtering configuration parameters can be written to the corresponding registers.

[0116] The original filter is configured according to preset tap coefficients to set the original filter's response frequency to obtain a target response frequency. It should be noted that the target response frequency represents the original gene sequencing signal that responds only to the corresponding frequency, so that the gene sequencing signal that meets the target response frequency can be extracted from the original gene sequencing signal.

[0117] The preset number of parameters configures the original filter module to modify the order of the original filter to the target order, so that the target order is the order of the target filter module. The preset number of points is the decimal position of the fixed-point number, and the target filter module is configured according to the decimal position of the fixed-point number. The dynamic range of the target filter module is adjusted to obtain the target dynamic range, and the target dynamic range can determine the accuracy of the target filter module.

[0118] In some embodiments, after determining the target response frequency, target order, and target dynamic range, the target response frequency, target order, and target dynamic range are directly configured on the original filter module to obtain a target filter module, so as to construct a target filter module that meets the requirements of filtering the original gene sequencing signal.

[0119] As mentioned above, before filtering each raw gene sequencing signal, a target filter module will be dynamically configured to dynamically adjust the filtering algorithm of the raw gene sequencing signal. This can better adapt to the noise characteristics of different gene sequencing signals, improve the adaptability and processing effect of gene sequencing signal filtering, and ensure superior data quality when processing various gene sequencing signals.

[0120] In some embodiments, after the target filter module is constructed, the original gene sequencing signal at the current time point is filtered by the target filter module. It should be noted that the target filter module uses a convolution operation module to complete the filtering process.

[0121] That is, in some embodiments, filtering the plurality of first gene sequencing signals by a target filter module to obtain a second gene sequencing signal may include:

[0122] Performing product processing on each first gene sequencing signal through a target filter module and a preset tap coefficient to obtain a fourth gene sequencing signal;

[0123] The target filter module calculates the sum of the plurality of fourth gene sequencing signals to obtain a second gene sequencing signal.

[0124] It should be noted that the target filter module is an FIR filter, and the function of the FIR filter needs to implement the FIR tap operation first, that is, the original gene sequencing signal of each tap is multiplied by its tap coefficient. In this embodiment, the convolution operation module includes a multiplier and an adder. In order to save the number of multipliers, the central symmetry of the tap coefficient is utilized, and two original gene sequencing signals that are symmetrical about the center are input at the same time. The tap coefficients of the FIR filter are arranged in a centrally symmetrical manner, so two first gene sequencing signals that are symmetrical about the center are input in parallel. Each first gene sequencing signal is multiplied by the corresponding tap coefficient by a multiplier to obtain a fourth gene sequencing signal.

[0125] In this embodiment, the two fourth gene sequencing signals are input to the adder for addition to obtain a second gene sequencing signal, and the second gene sequencing signal is a filtered gene sequencing signal.

[0126] Specifically, the processing flow for the first gene sequencing signal utilizes a symmetrical structural design, which reduces FPGA complexity and ensures that the phase characteristics of the FIR filter are linear within the FIR filter's response passband. As shown in Figure 5, the centrally symmetrical first gene sequencing signals are defined as Data_IN[i] and Data_IN[N-1]. The two first gene sequencing signals are multiplied by symmetrically arranged tap coefficients to produce two fourth gene sequencing signals, Data_XIN[i] and Data_XIN[N-1]. The two fourth gene sequencing signals, Data_XIN[i] and Data_XIN[N-1], are then added together to produce the second gene sequencing signal, Data_out[i].

[0127] It should be noted that after filtering the raw gene sequencing signal at the current time point, a preliminary gene sequencing signal is obtained, and processing of the preliminary gene sequencing signal continues at the next time point. It should be noted that, as shown in FIG6 , if conventional processing of raw gene sequencing signals is performed, it is necessary to wait until the preliminary gene sequencing signal is filtered, stored, and output to the host computer before processing the next raw gene sequencing signal. If a large number of raw gene sequencing signals are generated in real time, it will take a long time to complete the filtering of the raw gene sequencing signals.

[0128] Therefore, in this embodiment, a three-stage pipeline is set to complete the original gene sequencing signals at multiple time points. In other embodiments, a five-stage pipeline, a seven-stage pipeline, or a nine-stage pipeline can be set. This embodiment does not limit the way in which the filter processor performs filtering processing, and the timing design method of the filtering processing can be set according to demand.

[0129] In step S103, in the second-stage pipeline, the preliminary gene sequencing signal is stored in a preset register, and the original gene sequencing signal at the next time point is filtered to obtain a candidate gene sequencing signal; wherein the next time point is the time point after the current time point.

[0130] Step S104: In the third stage pipeline, the candidate gene sequencing signal is stored in a register, and the preliminary gene sequencing signal is output to a host computer.

[0131] It should be noted that the filtering process of the original gene sequencing signal mainly involves three processes, namely filtering, storage and output. For this reason, this embodiment sets a three-stage pipeline to complete the three operations of filtering, storage and outputting the signal, so as to improve the efficiency of filtering the original gene sequencing signal. Specifically, as shown in Figure 7, the first-stage pipeline sets n registers to configure the target filter module to filter the original gene sequencing signal at the current time point. In the second-stage pipeline, the filtered preliminary gene sequencing signal is first stored in n / 4 registers respectively, and the original gene sequencing signal at the next time point is filtered. Finally, in the third-stage pipeline, a register is used to upload the preliminary gene sequencing signal in the first-stage pipeline to the host computer, and the candidate gene sequencing signal of the second-stage pipeline is stored in n / 4 registers. At the same time, the original gene sequencing signal at the next time point is filtered through n registers. Therefore, in this embodiment, the three-stage pipeline is designed to intersperse the three steps of filtering, storing and outputting the original gene sequencing signal, which greatly improves the operating efficiency of the FIR filter and ensures the accuracy of the filtering process. Therefore, in this embodiment, a three-stage pipeline method is adopted to enable the FIR filter to complete the filtering process more quickly and accurately, thereby improving the overall performance of the system.

[0132] For example, in the first pipeline stage, 16 registers are set up to parallelly calculate each set of raw gene sequencing signals. In the second pipeline stage, 4 registers are set up to store the preliminary gene sequencing signals after filtering in the first pipeline stage. In the third pipeline stage, 1 register is set up to output the preliminary gene sequencing signals to the host computer. Therefore, 16 registers are set up for filtering, 4 registers are responsible for storing the filtered gene sequencing signals, and 1 register is used to output the gene sequencing signals to the host computer. Therefore, only 21 registers are needed to efficiently complete the filtering of the raw gene sequencing signals, without the need for costly hardware configuration, and can efficiently complete the filtering and output of a large number of gene sequencing signals.

[0133] Specifically, this embodiment uses the UDP protocol to output the filtered gene sequencing signal to the host computer. It should be noted that the UDP protocol has the characteristics of low latency and is a connectionless protocol that does not require a connection to be established, and data can be transmitted immediately. Therefore, this embodiment uses the UDP protocol to transmit the filtered gene sequencing signal to the host computer in real time, so that the host computer can process and analyze the filtered gene sequencing signal in a timely manner, thereby improving the efficiency of upstream analysis.

[0134] In the embodiment of the present application, steps S101 to S104 are shown, and multiple groups of original gene sequencing signals are collected at the same time and placed in a register. At the same time, each group of original gene sequencing signals is filtered in the first-level pipeline to obtain a preliminary gene sequencing signal. In the second-level pipeline, the filtered preliminary gene sequencing signal is directly stored in the register, and the original gene sequencing signal at the next time point is filtered. In the third-level pipeline, the preliminary gene sequencing signal is output to the host computer, and the candidate gene sequencing signal is stored in the register, and the original gene sequencing signal at the next time point is filtered. Therefore, each filtered gene sequencing signal is stored in the register, and the next gene sequencing signal is filtered. Thus, repeated filtering, storage, and output are performed to achieve pipeline filtering. There is no need to wait for a gene sequencing signal to complete filtering, storage, and output before filtering and storing the next gene sequencing signal. With pipeline processing of gene sequencing signals, hardware parallel performance is fully utilized, and the speed and efficiency of filtering of gene sequencing signals are improved, thereby improving the overall performance of the system.

[0135] In summary, as shown in FIG8 , FIG8 shows an overall flow chart of a method for filtering and processing gene sequencing signals. Therefore, the present application embodiment discloses:

[0136] Step 801: Capture the current change signal output by the nanopore sequencing device through a sensor array to obtain a preliminary current simulation signal;

[0137] Step 802 , amplifying the preliminary current analog signal through an integrating amplifier to obtain a candidate current analog signal;

[0138] Step 803: holding the candidate current analog signals through a sample-and-hold device to obtain multiple groups of target current analog signals;

[0139] Step 804: convert the target current analog signal into an original gene sequencing signal of a digital signal through an analog-to-digital conversion module;

[0140] Step 805: In the first stage pipeline, the normalization module performs offset processing on the original gene sequencing signal to obtain multiple first gene sequencing signals;

[0141] Step 806: Filter the first gene sequencing signal using a target filter module to obtain a second gene sequencing signal.

[0142] It should be noted that two first gene sequencing signals that are symmetrical about the center are input in parallel, and each original gene sequencing signal is multiplied by the corresponding tap coefficient through a multiplier to obtain a fourth gene sequencing signal. The two fourth gene sequencing signals are input into an adder for addition to obtain a second gene sequencing signal.

[0143] Step 807: performing offset and truncation processing on the second gene sequencing signal by a data offset module to obtain a preliminary gene sequencing signal;

[0144] Step S808: In the second stage pipeline, the preliminary gene sequencing signal is stored in a preset register, and the original gene sequencing signal at the next time point is filtered to obtain a candidate gene sequencing signal;

[0145] Step S808: In the third stage pipeline, the candidate gene sequencing signal is stored in a register, and the preliminary gene sequencing signal is output to the host computer.

[0146] It should be noted that in the second-stage pipeline, the filtered preliminary gene sequencing signals are first stored in multiple registers, and the original gene sequencing signals at the next time point are filtered. Finally, in the third-stage pipeline, a register is used to output the preliminary gene sequencing signals from the first-stage pipeline to the host computer. At the same time, the candidate gene sequencing signals from the second-stage pipeline are stored in a register, and the original gene sequencing signals at the next time point are filtered.

[0147] As shown above, in the embodiment, a three-stage pipeline design is used to complete the filtering, storage, and output of the original gene sequencing signal. The original gene sequencing signals at different time points are cross-filtered, stored, and output, thereby optimizing the speed and efficiency of the original gene sequencing signal processing, giving full play to the parallel performance of the register, and improving the overall performance of the system. At the same time, before filtering, a target filter module is configured according to the filtering requirements of different original gene sequencing signals to dynamically adjust the filtering algorithm of each original gene sequencing signal, which can better adapt to the noise characteristics of different gene sequencing signals and improve the adaptability and processing effect of the gene sequencing signal filtering processing.

[0148] Referring to FIG. 9 , an embodiment of the present application further provides a device for filtering and processing gene sequencing signals, which can implement the aforementioned method for filtering and processing gene sequencing signals. The device includes:

[0149] Quantization circuit 901 is used to collect the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current analog signals;

[0150] The analog-to-digital conversion module 902 is electrically connected to the quantization circuit and is used to perform analog-to-digital conversion on the target current analog signal to obtain multiple sets of original gene sequencing signals;

[0151] The target filter module 903 is electrically connected to the analog-to-digital conversion module and is used to filter the original gene sequencing signal to obtain the target gene sequencing signal;

[0152] The host computer 904 is communicatively connected to the target filter module and is used to receive the target gene sequencing signal.

[0153] The specific implementation of the gene sequencing signal filtering processing device is basically the same as the specific embodiment of the gene sequencing signal filtering processing method described above, and will not be repeated here.

[0154] The present application also provides a computer device comprising a memory and a processor. The memory stores a computer program, and the processor executes the computer program to implement the aforementioned method for filtering gene sequencing signals. The computer device can be any intelligent terminal, including a tablet computer and an in-vehicle computer.

[0155] Please refer to FIG10 , which illustrates the hardware structure of a computer device according to another embodiment. The computer device includes:

[0156] The processor 1001 can be implemented as a general-purpose CPU (Central Processing Unit), a microprocessor, an application-specific integrated circuit (ASIC), or one or more integrated circuits, and is used to execute relevant programs to implement the technical solutions provided in the embodiments of the present application;

[0157] The memory 1002 can be implemented in the form of a read-only memory (ROM), a static storage device, a dynamic storage device, or a random access memory (RAM). The memory 1002 can store an operating system and other application programs. When the technical solutions provided in the embodiments of this specification are implemented through software or firmware, the relevant program code is stored in the memory 1002 and is called by the processor 1001 to execute the filtering processing method for the gene sequencing signal of the embodiments of this application;

[0158] Input / output interface 1003, used to implement information input and output;

[0159] Communication interface 1004, used to implement communication interaction between this device and other devices, which can be achieved through wired means (such as USB, network cable, etc.) or wireless means (such as mobile network, WiFi, Bluetooth, etc.);

[0160] Bus 1005 , which transmits information between various components of the device (e.g., processor 1001 , memory 1002 , input / output interface 1003 , and communication interface 1004 );

[0161] The processor 1001 , the memory 1002 , the input / output interface 1003 and the communication interface 1004 are connected to each other in communication within the device via the bus 1005 .

[0162] An embodiment of the present application further provides a computer-readable storage medium storing a computer program, which, when executed by a processor, implements the above-mentioned filtering processing method for gene sequencing signals.

[0163] The memory, as a non-transient computer-readable storage medium, can be used to store non-transient software programs and non-transient computer executable programs. In addition, the memory may include a high-speed random access memory and may also include a non-transient memory, such as at least one disk storage device, a flash memory device, or other non-transient solid-state storage device. In some embodiments, the memory may optionally include a memory remotely arranged relative to the processor, and these remote memories may be connected to the processor via a network. Examples of the above-mentioned network include, but are not limited to, the Internet, an intranet, a local area network, a mobile communication network, and combinations thereof.

[0164] The embodiments described in the embodiments of this application are intended to more clearly illustrate the technical solutions of the embodiments of this application and do not constitute a limitation on the technical solutions provided by the embodiments of this application. Those skilled in the art will appreciate that with the evolution of technology and the emergence of new application scenarios, the technical solutions provided in the embodiments of this application are also applicable to similar technical problems.

[0165] Those skilled in the art will understand that the technical solutions shown in the figures do not constitute a limitation on the embodiments of the present application, and may include more or fewer steps than shown in the figures, or a combination of certain steps, or different steps.

[0166] The device embodiments described above are merely illustrative. The units described as separate components may or may not be physically separate, i.e., they may be located in one place or distributed across multiple network units. Some or all of the modules may be selected based on actual needs to achieve the objectives of this embodiment.

[0167] Those skilled in the art will appreciate that all or some of the steps in the methods, systems, and functional modules / units in the devices disclosed above may be implemented as software, firmware, hardware, or appropriate combinations thereof.

[0168] The terms "first", "second", "third", "fourth", etc. (if any) in the specification of the present application and the above-mentioned drawings are used to distinguish similar objects and are not necessarily used to describe a specific order or sequential order. It should be understood that the data used in this way can be interchangeable where appropriate, so that the embodiments of the present application described herein can be implemented in an order other than those illustrated or described herein. In addition, the terms "including" and "having" and any variations thereof are intended to cover non-exclusive inclusions, for example, a process, method, system, product or device that includes a series of steps or units is not necessarily limited to those steps or units clearly listed, but may include other steps or units that are not clearly listed or inherent to these processes, methods, products or devices.

[0169] It should be understood that in this application, "at least one (item)" means one or more, and "plurality" means two or more. "And / or" is used to describe the association relationship of associated objects, indicating that three relationships may exist. For example, "A and / or B" can mean: only A exists, only B exists, and A and B exist at the same time, where A and B can be singular or plural. The character " / " generally indicates that the previous and next associated objects are in an "or" relationship. "At least one of the following items" or similar expressions refers to any combination of these items, including any combination of single items or plural items. For example, at least one of a, b or c can mean: a, b, c, "a and b", "a and c", "b and c", or "a and b and c", where a, b, c can be single or multiple.

[0170] In the several embodiments provided in this application, it should be understood that the disclosed devices and methods can be implemented in other ways. For example, the device embodiments described above are merely schematic. For example, the division of the above-mentioned units is only a logical function division. In actual implementation, there may be other division methods, such as multiple units or components can be combined or integrated into another system, or some features can be ignored or not executed. Another point is that the mutual coupling or direct coupling or communication connection shown or discussed can be through some interfaces, indirect coupling or communication connection of devices or units, which can be electrical, mechanical or other forms.

[0171] The units described above as separate components may or may not be physically separate, and the components shown as units may or may not be physical units, that is, they may be located in one place or distributed across multiple network units. Some or all of these units may be selected according to actual needs to achieve the purpose of the solution of this embodiment.

[0172] In addition, the functional units in the various embodiments of the present application may be integrated into a single processing unit, or each unit may exist physically separately, or two or more units may be integrated into a single unit. The aforementioned integrated units may be implemented in the form of hardware or software functional units.

[0173] If the integrated unit is implemented in the form of a software functional unit and sold or used as an independent product, it can be stored in a computer-readable storage medium. Based on this understanding, the technical solution of the present application, or the part that contributes to the prior art, or all or part of the technical solution can be embodied in the form of a software product, which is stored in a storage medium and includes multiple instructions for enabling a computer device (which can be a personal computer, server, or network device, etc.) to execute all or part of the steps of the methods of various embodiments of the present application. The aforementioned storage medium includes: various media that can store programs, such as a USB flash drive, a mobile hard disk, a read-only memory (ROM), a random access memory (RAM), a magnetic disk or an optical disk.

[0174] The preferred embodiments of the present invention are described above with reference to the accompanying drawings, but are not intended to limit the scope of the present invention. Any modifications, equivalent substitutions, and improvements made by those skilled in the art without departing from the scope and essence of the present invention should be within the scope of the present invention.

Claims

1. A method for filtering gene sequencing signals, characterized in that: The method comprises: Based on the current changes generated by different bases passing through the nanopore, multiple sets of original gene sequencing signals are obtained; In the first stage pipeline, each set of the original gene sequencing signals at the current time point is filtered to obtain a preliminary gene sequencing signal; In the second-stage pipeline, the preliminary gene sequencing signal is stored in a preset register, and the original gene sequencing signal at the next time point is filtered to obtain a candidate gene sequencing signal; wherein the next time point is the time point after the current time point; In the third stage pipeline, the candidate gene sequencing signal is stored in the register, and the preliminary gene sequencing signal is output to the host computer.

2. The method according to claim 1, characterized in that The filtering process of each group of the original gene sequencing signals at the current time point to obtain a preliminary gene sequencing signal includes: Performing offset processing on each group of the original gene sequencing signals at the current time point through a normalization module to obtain multiple first gene sequencing signals; Performing filtering processing on the plurality of first gene sequencing signals through a target filter module to obtain a second gene sequencing signal; The second gene sequencing signal is subjected to offset and truncation processing by a data offset module to obtain the preliminary gene sequencing signal.

3. The method according to claim 2, characterized in that The filtering process of the plurality of first gene sequencing signals by a target filter module to obtain a second gene sequencing signal includes: Performing product processing on each of the first gene sequencing signals using the target filter module and a preset tap coefficient to obtain a fourth gene sequencing signal; The target filter module calculates the sum of the plurality of fourth gene sequencing signals to obtain the second gene sequencing signal.

4. The method according to claim 2, characterized in that Before filtering the plurality of first gene sequencing signals by the target filter module to obtain a second gene sequencing signal, the method further includes: Obtaining filtering requirement information of the original gene sequencing signal; Filtering target filtering configuration parameters from preset candidate filtering configuration parameters according to the filtering requirement information; The preset original filter module is configured according to the target filter configuration parameters to obtain the target filter module.

5. The method according to claim 4, characterized in that The target filter configuration parameters include: preset tap coefficients, preset parameter quantity and preset point number information; the preset original filter module is configured and processed according to the target filter configuration parameters to obtain the target filter module, including Setting a preset response frequency of the original filter module according to the preset tap coefficient to obtain a target response frequency; Setting the order of the original filter module according to the preset number of parameters to obtain a target order; Setting the dynamic range of the original filter module according to the preset number of points to obtain a target dynamic range; The original filter module is configured according to the target response frequency, the target order and the target dynamic range to obtain a target filter module.

6. The method according to claim 1, characterized in that The original gene sequencing signal is output by a quantization circuit, and the quantization circuit includes: a sampling module and an analog-to-digital conversion module; the current changes generated by different bases passing through the nanopore to obtain multiple groups of original gene sequencing signals include: The sampling module collects the current changes generated by different bases passing through the nanopore to obtain multiple groups of target current simulation signals; The analog-to-digital conversion module performs analog-to-digital conversion on the multiple sets of target current analog signals to obtain multiple sets of original gene sequencing signals.

7. The method according to claim 6, characterized in that The sampling module includes: a switch unit, an integrating amplifier and a sample-and-hold unit; the sampling module collects the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current analog signals, including: The switching unit collects the current changes generated by different bases passing through the nanopore to obtain multiple groups of preliminary current simulation signals; amplifying each of the preliminary current analog signals by the integrating amplifier to obtain a candidate current analog signal; The candidate current analog signals are held by the sample and hold device to obtain multiple groups of target current analog signals.

8. A filtering and processing device for gene sequencing signals, characterized in that: A filtering processing device for a gene sequencing signal according to any one of claims 1 to 7, the device comprising: A quantization circuit is used to collect the current changes generated by different bases passing through the nanopore to obtain multiple sets of target current simulation signals; an analog-to-digital conversion module, electrically connected to the quantization circuit, for performing analog-to-digital conversion on the target current analog signal to obtain multiple sets of original gene sequencing signals; a target filter module, electrically connected to the analog-to-digital conversion module, for performing filtering processing on the original gene sequencing signal to obtain a target gene sequencing signal; The host computer is communicatively connected to the target filter module and is used to receive the target gene sequencing signal.

9. A computer device, characterized in that: The computer device includes a memory and a processor, the memory stores a computer program, and the processor implements the filtering processing method for gene sequencing signals according to any one of claims 1 to 7 when executing the computer program.

10. A computer-readable storage medium storing a computer program, characterized in that: When the computer program is executed by a processor, the filtering processing method of the gene sequencing signal according to any one of claims 1 to 7 is implemented.

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