Chromosome structure variation recognition device

Abstract

The embodiment of the invention discloses a chromosome structure variation recognition device. The device comprises a genome position acquisition module used for acquiring a genome position of a target sample for a karyotype result of chromosome structure variation; the bar code information obtaining module is used for sliding windows on chromosomes corresponding to the genome positions to obtain bar code information of bar codes corresponding to the windows respectively; the candidate structure variation region determination module is used for determining a shared bar code proportion according to the bar code information corresponding to every two target windows in all the windows, so as to determine a candidate structure variation region on the chromosome according to the determined shared bar code proportion; and the chromosome structure variation recognition module is used for obtaining a target structure variation region on the chromosome according to the window position corresponding to each candidate structure variation region and the strip position of the karyotype strip on the chromosome. According to the technical scheme provided by the embodiment of the invention, the sensitivity of chromosome structure variation recognition can be improved.

Description

Technical Field

[0001] The embodiments of the present invention relate to the field of biological information technology, and in particular to a device for identifying chromosome structural variation. Background Art

[0002] Assisted reproductive technology (ART), as one of the most effective methods for treating infertility, can help infertile families realize their desire to have children.

[0003] On this basis, the development of next-generation sequencing (NGS) technology has promoted the application of preimplantation genetic testing (PGT) in ART, which helps to reduce the birth of children with genetic diseases. In view of this, NGS technology, especially long fragment (linked-reads)-based NGS technology, can be used to detect (i.e. identify) chromosome structural variation (SV) before embryo implantation in infertile people.

[0004] However, there is currently a problem of low sensitivity in the identification of chromosomal SVs, which needs to be resolved. Summary of the invention

[0005] The embodiment of the present invention provides a device for identifying chromosome structural variation, which solves the problem of low sensitivity in chromosome SV identification.

[0006] According to one aspect of the present invention, a device for identifying chromosome structural variation is provided, which may include:

[0007] A genome position acquisition module is used to obtain the genome position of the karyotype result of the target sample for the chromosome structural variation for the target sample to be identified with the chromosome structural variation;

[0008] A barcode information obtaining module is used to slide a window on the chromosome corresponding to the genome position to obtain barcode information of the barcode corresponding to each window;

[0009] A candidate structural variation region determination module is used to determine the shared barcode ratio for each two target windows in all windows according to the barcode information corresponding to the two target windows, so as to determine the candidate structural variation region on the chromosome according to the determined shared barcode ratios;

[0010] The chromosome structural variation identification module can be used to obtain the window position of each window corresponding to the candidate structural variation region and the band position of the karyotype band on the chromosome for each candidate structural variation region obtained, so as to obtain the target structural variation region on the chromosome according to the window position and band position corresponding to each candidate structural variation region.

[0011] The technical solution of the embodiment of the present invention is to obtain the genomic position of the karyotype result of the target sample for SV identification through the genome position acquisition module, so as to find the key genome for identifying SV from all genomes, or to find the key chromosome for identifying SV from all chromosomes; to obtain the barcode information of the barcode corresponding to each window through the barcode information acquisition module; and to determine the candidate structural variation region for each two target windows in all windows according to the two target windows. The barcode information corresponding to the target windows respectively determines the shared barcode ratio, which can characterize the possibility of SV occurring in the region covered by the two target windows on the chromosome, and thus the candidate SV region on the chromosome can be determined according to the determined shared barcode ratios; further, through the chromosome structural variation recognition module, for each candidate SV region, the window position of each window corresponding to the candidate SV region and the band position of the karyotype band on the chromosome can be obtained, and the positional relationship between these two positions can characterize the possibility of SV occurring in the candidate SV region to a certain extent, so the target SV region on the chromosome can be obtained according to the window position and band position corresponding to each candidate SV region. The above technical solution can improve the sensitivity of chromosome SV recognition.

[0012] It should be understood that the contents described in this section are not intended to identify the key or important features of the embodiments of the present invention, nor are they intended to limit the scope of the present invention. Other features of the present invention will become easily understood through the following description. BRIEF DESCRIPTION OF THE DRAWINGS

[0013] In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the following briefly introduces the drawings required for use in the description of the embodiments. Obviously, the drawings described below are only some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without creative work.

[0014] Figure 1 is a structural block diagram of a device for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0015] Figure 2 is a structural block diagram of another device for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0016] Figure 3a is a schematic diagram of a shared barcode ratio obtained after comparing any two target windows on chr1 and chr11 in another apparatus for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0017] Figure 3b is a schematic diagram of merging two regional windows on chr1 and chr11 in another device for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0018] Figure 4 is a structural block diagram of another device for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0019] Figure 5a is a schematic diagram of a shared barcode ratio obtained after comparing any two target windows on chr2 in another apparatus for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0020] Figure 5b is a schematic diagram of merging two regional windows on chr2 in another device for identifying chromosome structural variation provided according to an embodiment of the present invention;

[0021] Figure 6 It is a structural block diagram of another device for identifying chromosome structural variation provided according to an embodiment of the present invention. DETAILED DESCRIPTION

[0022] In order to enable those skilled in the art to better understand the scheme of the present invention, the technical scheme in the embodiments of the present invention will be clearly and completely described below in conjunction with the drawings in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work should fall within the scope of protection of the present invention.

[0023] It should be noted that the terms "first", "second", etc. in the specification and claims of the present invention and the above-mentioned drawings are used to distinguish similar objects, and are not necessarily used to describe a specific order or sequence. It should be understood that the data used in this way can be interchangeable where appropriate, so that the embodiments of the present invention described herein can be implemented in an order other than those illustrated or described herein. The situations of "target", "original", etc. are similar and will not be repeated here. 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 comprising 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.

[0024] Figure 1 This is a structural block diagram of a device for identifying chromosome structural variation provided by an embodiment of the present invention. This embodiment can be applied to the case of chromosome SV identification, and is particularly applicable to the case of chromosome SV identification before embryo implantation for infertile people based on linked-reads NGS technology.

[0025] See also Figure 1 The device for identifying chromosome structural variation according to the embodiment of the present invention comprises: a genome position acquisition module 10, a barcode information acquisition module 11, a candidate structural variation region determination module 12 and a chromosome structural variation identification module 13; wherein,

[0026] The genome position acquisition module 10 is used to acquire the genome position of the karyotype result of the target sample for the chromosome structural variation for the target sample to be subjected to chromosome structural variation identification;

[0027] The barcode information obtaining module 11 is used to slide the window on the chromosome corresponding to the genome position to obtain the barcode information of the barcode corresponding to each window;

[0028] The candidate structural variation region determination module 12 is used to determine the shared barcode ratio for each two target windows in all the windows according to the barcode information respectively corresponding to the two target windows, so as to determine the candidate structural variation region on the chromosome according to the determined shared barcode ratios;

[0029] The chromosome structural variation identification module 13 is used to obtain the window position of each window corresponding to each candidate structural variation region and the band position of the karyotype band on the chromosome for each candidate structural variation region obtained, so as to obtain the target structural variation region on the chromosome according to the window position and band position corresponding to each candidate structural variation region.

[0030] Among them, the target sample can be understood as a sample to be identified as a chromosome SV (hereinafter referred to as SV). The karyotype result can be understood as the result of the karyotype of the target sample for the SV. The genome position can be understood as the position of the karyotype result on the genome. The genome position is obtained by the genome position acquisition module 10, which facilitates finding the key genome for identifying SV from the entire genome. Exemplarily, assuming that the karyotype result is t(1;11)(1q31.2;11q25), it is pre-judged that the region where the SV occurs is the q arm of chr1 and the q arm of chr11, wherein the genomic position corresponding to the q arm of chr1 is chr1:125000000-249250621, and the genomic position corresponding to the q arm of chr11 is chr11:53700000-135006516.

[0031] Chromosome can be understood as the chromosome where the genome pointed to by the genome position is located, and can be further understood as the partial chromosome of the genome contained in the chromosome. The number of the chromosome can be one or two, which is related to the specific type of SV (such as inversion, balanced translocation, deletion or duplication, etc.), which is not specifically limited here. Exemplarily, the SV given in the above example is a translocation, which involves two chromosomes, which are chromosome 1 and chromosome 11.

[0032] Through the barcode information acquisition module 11, a window of fixed size is used to slide on the chromosome to obtain multiple windows, each of which covers a part of the chromosome. Further, since the target sample has been sequenced in its entire genome, the barcode information (i.e., barcode information) of the barcode corresponding to each window can be obtained through the barcode information acquisition module 11. The barcode information can be, for example, the number of barcodes and / or barcode ID, etc. Exemplarily, the chromosome, the starting position of the window, the ending position of the window, the number of barcodes in the window, and the barcode ID, etc. can be output at this time. This can be set according to actual needs and is not specifically limited here.

[0033] The two target windows can be understood as two paired windows in all windows. For example, when the number of chromosomes is two, it can be considered that each window on one chromosome is paired one by one with each window of the other chromosome. For example, there are window A and window B on one chromosome, and window C and window D on the other chromosome. Then window A and window C, window A and window D, window B and window C, and window B and window D are two target windows respectively. When the number of chromosomes is one, it can be considered that each window on the chromosome is paired one by one with each window on the chromosome that has not been paired with the window. For example, there are window A, window B and window C on one chromosome. Then window A and window B, window A and window C, and window B and window C are two target windows respectively.

[0034] For the two target windows described above, multiple pairs of the two target windows can be found from all the windows. Here, the candidate structural variation region determination module 12 is used to determine the shared barcode ratio for each two target windows according to the barcode information corresponding to the two target windows. The shared barcode ratio can be understood as the ratio of shared barcodes (i.e., shared barcodes). The shared barcode can be understood as the barcode shared (i.e., shared) by the two target windows. Then, according to the shared barcode ratios determined for the two different target windows, the candidate structural variation regions (i.e., candidate SV regions) where SVs may occur on the chromosome are determined. The number of the candidate SV regions can be one or more, which is not specifically limited here.

[0035] The candidate SV region corresponds to at least two windows in all windows, that is, the candidate SV region can be understood as the region covered by the at least two windows on the chromosome. The at least two windows have respective window positions on the chromosome, and the window positions can be represented by the starting position and the ending position of the corresponding window. The karyotype band can be understood as the region where the SV may occur determined on the chromosome according to the karyotype results, and the position of the karyotype band on the chromosome is called the band position.

[0036] Through the chromosome structural variation identification module 13, for each candidate SV region obtained, the window position and band position corresponding to the candidate SV region are obtained, and then the target structural variation region (i.e., the target SV region) on the chromosome is obtained based on the window position and band position corresponding to each candidate SV region.

[0037] The technical solution of the embodiment of the present invention is to obtain the genomic position of the karyotype result of the target sample for SV identification through the genome position acquisition module, so as to find the key genome for identifying SV from all genomes, or to find the key chromosome for identifying SV from all chromosomes; to obtain the barcode information of the barcode corresponding to each window through the barcode information acquisition module; and to determine the candidate structural variation region for each two target windows in all windows according to the two target windows. The barcode information corresponding to the target windows respectively determines the shared barcode ratio, which can characterize the possibility of SV occurring in the region covered by the two target windows on the chromosome, and thus the candidate SV region on the chromosome can be determined according to the determined shared barcode ratios; further, through the chromosome structural variation recognition module, for each candidate SV region, the window position of each window corresponding to the candidate SV region and the band position of the karyotype band on the chromosome can be obtained, and the positional relationship between these two positions can characterize the possibility of SV occurring in the candidate SV region to a certain extent, so the target SV region on the chromosome can be obtained according to the window position and band position corresponding to each candidate SV region. The above technical solution can improve the sensitivity of chromosome SV recognition.

[0038] An optional technical solution, the above identification device further includes:

[0039] A target file generation module is used to obtain the whole genome sequencing data of the target sample and compare the whole genome sequencing data with the preset reference genome to generate a target file;

[0040] Correspondingly, the barcode information obtaining module is specifically used to perform a sliding window on the chromosome corresponding to the genomic position, so as to obtain the barcode information of the barcode corresponding to each window according to the read segment information corresponding to the genomic position extracted from the target file.

[0041] Among them, the whole genome sequencing data can be understood as the data obtained after whole genome sequencing of the target sample. The whole genome sequencing data is compared with the preset reference genome, and a target file is generated based on the comparison. The target file records the read information of the whole genome.

[0042] The target file generation module is used to obtain whole genome sequencing data and compare the whole genome sequencing data with the reference genome to generate a target file.

[0043] On this basis, the barcode information can be obtained through the module to extract the reads information corresponding to the genome position from the target file, that is, to extract the reads information of the genome represented by the genome position, and then obtain the barcode information corresponding to each window based on the reads information.

[0044] The above technical solution obtains reads information by acquiring and comparing whole genome sequencing data, and the reads information is the key to obtaining barcode information.

[0045] In order to better understand the above technical solution, the following is an exemplary explanation with reference to a specific example. For example, here we take the target sample of balanced translocation No. 1 and No. 11 for SV identification as an example, and its karyotype result is t(1;11)(1q31.2;11q25). The specific steps related to the above technical solution are as follows;

[0046] 1. Library construction and sequencing:

[0047] 1) Library construction, which mainly includes the following steps: extraction and dilution of genomic deoxyribonucleic acid (DNA) - addition of fragmentation enzyme - hybridization with magnetic beads with molecular tags - fragmentation enzyme release - adapter ligation - library amplification, and sequencing based on the library.

[0048] 2) Sequencing: the sequencing type is paired-end sequencing 100, and the number of sequencing sequences is about 80 Gb, so as to obtain whole genome sequencing data, which is recorded in the fastq file.

[0049] 2. Data standard analysis:

[0050] 1) Data preprocessing: According to the characteristics of the labeling, the barcode molecular label sequence and fixed sequence in the fastq file of read2 are removed through the barcode table, and the barcode information is marked on the readname of the fastq file.

[0051] 2) Alignment: Filter low-quality sequences from the separated fastq files, align the filtered fastq files to the reference genome (hg19), and generate a bam file. The aligned sequences are PCR deduplicated and BQSR aligned to form a bam file (i.e., the target file mentioned above).

[0052] 3. Determination of the genomic position of the karyotype results: According to the karyotype results t(1;11)(1q31.2;11q25), it is pre-judged that the SV occurs on the q arm of chr1 and the q arm of chr11, and the corresponding genomic positions are chr1:125000000-249250621 and chr11:53700000-135006516, respectively.

[0053] 4. Extraction and organization of barcode information:

[0054] 1) Extract the reads information of chr1:125000000-249250621 from the bam file finally formed in 2.2 to form file 1 corresponding to chromosome 1, and extract the reads information of chr11:53700000-135006516 to form file 11 corresponding to chromosome 11. Both files record at least one of the name of the aligned sequence (query template name, QNAME), the specific alignment information of the reads (FLAG), the name of the reference sequence during alignment (Reference sequence NAME of the alignment, RNAME), the position of the read aligned to the reference genome (POS), the quality of the corresponding reference sequence (MAPing Quality, MAPQ), the position of the other read aligned to the reference genome in the double-end sequencing (PNEXT) and the length of the library (insert DNA size, TLEN).

[0055] 2) Perform this step separately according to the two files obtained in 4.1. Slide the genome position according to the 200kb window, record the number of barcodes and barcode ID under each window, and the final output result may include at least one of the chromosome, the starting position, the ending position, and the number of barcodes and barcode ID in the window.

[0056] Figure 2It is a structural block diagram of another device for identifying chromosome structural variation provided by an embodiment of the present invention. This embodiment is optimized based on the above-mentioned technical solutions. In this embodiment, optionally, the candidate structural variation region determination module includes a shared barcode ratio determination submodule and a candidate structural variation region determination submodule; wherein the shared barcode ratio determination submodule is used to determine the shared barcode ratio for each two target windows in all windows according to the barcode information corresponding to the two target windows respectively; the candidate structural variation region determination submodule is used to determine the candidate structural variation region on the chromosome according to the obtained total shared barcode ratio. Among them, the explanations of the terms that are the same as or corresponding to the above-mentioned embodiments are not repeated here.

[0057] For details, see Figure 2 The chromosome structural variation identification device described in this embodiment includes: a genome position acquisition module 20, a barcode information acquisition module 21, a candidate structural variation region determination module 22 and a chromosome structural variation identification module 23; wherein the candidate structural variation region determination module 22 includes a shared barcode ratio determination submodule 221 and a candidate structural variation region determination submodule 222;

[0058] A genome position acquisition module 20 is used to acquire the genome position of the karyotype result of the target sample for the chromosome structural variation identification for the target sample;

[0059] The barcode information obtaining module 21 is used to slide the window on the chromosome corresponding to the genome position to obtain the barcode information of the barcode corresponding to each window;

[0060] The shared barcode ratio determination submodule 221 is used to determine the shared barcode ratio for every two target windows in all windows according to the barcode information respectively corresponding to the two target windows;

[0061] A candidate structural variation region determination submodule 222 is used to determine the candidate structural variation region on the chromosome according to the obtained ratio of all shared barcodes;

[0062] The chromosome structural variation identification module 23 is used to obtain the window position of each window corresponding to each candidate structural variation region and the band position of the karyotype band on the chromosome for each candidate structural variation region obtained, so as to obtain the target structural variation region on the chromosome according to the window position and band position corresponding to each candidate structural variation region.

[0063] Among them, the shared barcode ratio determination submodule 221 determines the shared barcode ratio according to the barcode information corresponding to the two target windows respectively; then, the candidate structural variation region determination submodule 222 determines one or more candidate SV regions according to the obtained shared barcode ratios.

[0064] The technical solution of the embodiment of the present invention realizes accurate determination of candidate SV regions through the cooperation between the shared barcode ratio determination submodule and the candidate structural variant region determination submodule.

[0065] In an optional technical solution, the shared barcode ratio determination submodule includes a quantity determination unit and a shared barcode ratio determination unit;

[0066] The quantity determination unit is used to determine, for every two target windows in all the windows, a first quantity of shared barcodes between the two target windows and a second quantity of different types of barcodes involved in the two target windows according to the barcode information respectively corresponding to the two target windows;

[0067] The shared barcode ratio determining unit is used to determine the shared barcode ratio of the shared barcodes according to the first quantity and the second quantity.

[0068] Here, taking any two target windows as an example, the shared barcode (i.e., shared barcode) can be understood as the barcode existing in both target windows, that is, the barcode in the intersection between the barcode in one target window and the barcode in the other target window of the two target windows. The first number can be understood as the number of the shared barcodes.

[0069] The second number can be understood as the number of different types of barcodes (ie, different barcodes) involved in the two target windows, that is, the number of barcodes in the union of the barcode in one target window and the barcode in the other target window of the two target windows.

[0070] The quantity determination unit obtains the first quantity and the second quantity according to the barcode information corresponding to the two target windows, and then determines the shared barcode ratio according to the first quantity and the second quantity by the shared barcode ratio determination unit, for example, taking the ratio of the first quantity to the second quantity as the shared barcode ratio.

[0071] The above technical solution realizes accurate and rapid determination of the shared barcode ratio between the two target windows by determining the first number of shared barcodes between the two target windows and the second number of different types of barcodes involved in the two target windows.

[0072] In another optional technical solution, the candidate structure variation region determination submodule includes a shared barcode ratio filtering unit and a candidate structure variation region determination unit;

[0073] The shared barcode ratio filtering unit is used to filter all the obtained shared barcode ratios based on a preset ratio threshold to obtain the retained shared barcode ratio;

[0074] The candidate structural variation region determination unit is used to determine the candidate structural variation region on the chromosome based on two target windows corresponding to each retained shared barcode ratio.

[0075] Among them, the ratio threshold can be understood as a pre-set threshold related to the shared barcode ratio. In combination with the application scenarios that may be involved in the embodiments of the present invention, optionally, the ratio threshold can be determined based on the theoretical shared barcode ratio of the target SV area where the SV occurs.

[0076] Two different target windows correspond to their own shared barcode ratios. After all shared barcode ratios are obtained, the shared barcode ratio filtering unit can filter all shared barcode ratios based on the ratio threshold. For example, the shared barcode ratios less than or equal to the ratio threshold can be filtered out, that is, the shared barcode ratios greater than the ratio threshold are retained to obtain the retained shared barcode ratios, that is, the shared barcode ratios retained after filtering in the total shared barcode ratios. Further, the candidate structural variation region determination unit determines the candidate SV region based on the two target windows corresponding to each retained shared barcode ratio.

[0077] The above technical solution filters the corresponding two target windows by filtering the shared barcode ratio, and then filters the corresponding region on the chromosome, which is the region where SV will not occur, thereby achieving accurate determination of candidate SV regions where SV may occur.

[0078] On this basis, optionally, a candidate structure variation region determination unit is specifically used to:

[0079] For each retained shared barcode ratio obtained, two target windows corresponding to the retained shared barcode ratio are respectively used as region windows;

[0080] In the case that there are adjacent region windows in positions in all the obtained region windows, the adjacent region windows are merged, and all the region windows are updated based on the merged result;

[0081] Based on the entire region window, candidate structural variation regions on the chromosome are determined.

[0082] The area window can be understood as a target window corresponding to the ratio of the shared barcode. Adjacent area windows can be understood as two or more area windows that are adjacent in position among all area windows. The adjacent area windows may exist in one or more groups, which is related to the actual situation and is not specifically limited here.

[0083] It can be understood that the adjacent region windows correspond to adjacent regions on the chromosome. Therefore, the adjacent region windows can be merged to connect the adjacent regions together, so that the connected regions are regarded as a candidate SV region, rather than treating each region as a candidate SV region separately. This, combined with subsequent steps, helps to improve the accuracy of determining the target SV region.

[0084] Another optional technical solution is that the shared barcode ratio determination submodule is also used to:

[0085] When there are two chromosomes, each window on one chromosome is paired with each window on another chromosome one by one, and the two paired windows are used as two target windows;

[0086] When the number of chromosomes is one and the p arm and q arm of the chromosome are involved, each window on the p arm is paired with each window on the q arm one by one, and the two paired windows are used as two target windows;

[0087] When the number of chromosomes is one and the same arm of the chromosome is involved, each window on the arm is paired one by one with each window in all windows that has not been paired with the window, and the two paired windows are used as two target windows.

[0088] Among them, when two chromosomes are involved, that is, two arms of different chromosomes are involved, each window on one chromosome can be paired one by one with each window on the other chromosome, that is, each window on one arm can be paired one by one with each window on the other arm, and each pair of two windows obtained can be used as two target windows respectively to obtain multiple pairs of two target windows.

[0089] When the p arm and q arm of a chromosome are involved, each window on the p arm can be paired with each window on the q arm one by one, and the two paired windows are used as two target windows.

[0090] In the case of involving the same arm of a chromosome, taking any window on the arm as an example, the window can be paired one by one with the remaining windows on the arm. The remaining windows can be understood as windows that have not been paired with the window, and then the two paired windows are used as two target windows.

[0091] The above technical solution realizes the accurate determination of two target windows under different circumstances.

[0092] In order to better understand the various technical solutions in the embodiments of the present invention as a whole, the following description will be continued based on the above example (i.e., SV identification of target samples of balanced translocation No. 1 and No. 11).

[0093] 5. SV identification and visualization:

[0094] 1) According to the two files obtained in 4.1, for each window on chr1 q (here referred to as window 1), compare the window 1 with all windows on chr11 q (here referred to as window 2), and the final result is window 1, window 2, the number of barcodes under window 1, the number of barcodes under window 2, the first number of shared barcodes between the two windows, and the shared barcode ratio. The above-mentioned window 1 and window 2 are the two paired target windows, and the specific calculation method of the shared barcode ratio is as follows;

[0095] Window1barcode={barcode1, barcode2, barcode3, barcode4, ...}## represents the barcode set of window 1;

[0096] Window2barcode={barcode1, barcode2, barcode3, barcode4, ...}## represents the barcode set of window 2;

[0097] Intersect Barcode=Window1barcode∩Window2barcode## represents the intersection of the barcodes of window 1 and window 2, then |Intersect Barcode| represents the first number of barcodes in the intersection;

[0098] Union barcode=Window1barcode∪Window2barcode## represents the barcode union of window 1 and window 2, then |Union barcode| represents the second number of barcodes in the union;

[0099] Barcode overlap ratio = |Intersect Barcode| / |Union barcode|## indicates the ratio of shared barcodes between window 1 and window 2.

[0100] 2) According to the ratio threshold, filter the barcode overlap ratios obtained in 5.1, and retain the barcode overlap ratios that are greater than the ratio threshold.

[0101] 3) For the area windows corresponding to the barcode overlap ratios retained in 5.2, if there are area windows adjacent in position, the adjacent area windows are merged.

[0102] 4) Visualization results see Figure 3a and Figure 3b .in, Figure 3a The horizontal and vertical axes represent the target windows on the two chromosomes chr1 and chr11 for comparison, respectively. Each point represents two target windows for comparison, and the color of the point represents the size of the barcode overlap ratio (i.e., Barcode_overlap_ratio). Figure 3b is Figure 3a On this basis, the merging process of the two regional windows is indicated by a blue box.

[0103] Figure 4 It is a structural block diagram of another device for identifying chromosome structural variation provided by an embodiment of the present invention. This embodiment is optimized based on the above-mentioned technical solutions. In this embodiment, optionally, the chromosome structural variation recognition module is also used to: obtain the existence of target reads on the candidate structural variation region, so as to obtain the target structural variation region on the chromosome according to the window position, band position and existence corresponding to each candidate structural variation region, wherein the target read includes a read pair and / or a split read. Among them, the explanation of the terms that are the same or corresponding to the above-mentioned embodiments will not be repeated here.

[0104] For details, see Figure 4 The chromosome structural variation identification device described in this embodiment includes: a genome position acquisition module 30, a barcode information acquisition module 31, a candidate structural variation region determination module 32 and a chromosome structural variation identification module 33; wherein,

[0105] A genome position acquisition module 30 is used to acquire the genome position of the karyotype result of the target sample for the chromosome structural variation identification for the target sample;

[0106] The barcode information obtaining module 31 is used to slide the window on the chromosome corresponding to the genome position to obtain the barcode information of the barcode corresponding to each window;

[0107] The candidate structural variation region determination module 32 is used to determine the shared barcode ratio for each two target windows in all the windows according to the barcode information respectively corresponding to the two target windows, so as to determine the candidate structural variation region on the chromosome according to the determined shared barcode ratios;

[0108] The chromosome structural variation identification module 33 is used to obtain, for each candidate structural variation region obtained, the window position of each window corresponding to the candidate structural variation region, the existence of the target read segment on the candidate structural variation region, and the band position of the karyotype band on the chromosome, so as to obtain the target structural variation region on the chromosome according to the window position, band position and existence corresponding to each candidate structural variation region, wherein the target read segment includes a read segment pair and / or a split read segment.

[0109] According to practical experience, if a target read (i.e., target reads) exists in a candidate SV region, then there is a high probability that SV will occur in the candidate SV region, so the target reads can be understood as evidence supporting SV. In combination with the application scenarios that may be involved in the embodiments of the present invention, the target reads can be read pairs and / or split reads, etc., which are not specifically limited here.

[0110] The existence of target reads on the candidate SV region is obtained, and the existence can characterize whether the target reads exist on the candidate SV region. In this way, the target SV region can be obtained according to the window position, stripe position and existence corresponding to each candidate SV region.

[0111] The technical solution of the embodiment of the present invention determines whether the candidate SV region is the target SV region by judging whether there are target reads on the candidate SV region, and further determines whether the candidate SV region is the target SV region based on the existence of the target reads. The introduction of target reads can significantly improve the accuracy of determining the target SV region.

[0112] In an optional technical solution, the chromosome structural variation recognition module includes a regional scoring submodule and a chromosome structural variation recognition submodule; wherein the regional scoring submodule includes the following three units:

[0113] A position score obtaining unit is used to obtain, for each candidate structural variation region, the window position of each window corresponding to the candidate structural variation region and the band position of the karyotype band on the chromosome, and obtain a position score according to the window position and the band position;

[0114] A read score obtaining unit, for obtaining, for each candidate structural variation region, the presence of a target read on the candidate structural variation region, and obtaining a read score according to the presence;

[0115] A target score obtaining unit, for obtaining a target score for each candidate structural variation region according to a position score and a read score corresponding to the candidate structural variation region;

[0116] Among them, the chromosome structural variation identification submodule is used to obtain the target structural variation region on the chromosome according to the target score corresponding to each candidate structural variation region.

[0117] Among them, for each candidate SV region, a unit can be obtained by position scoring, and a position score can be performed according to the window position and band position corresponding to the candidate SV region, and a unit can be obtained by reading segment scoring, and a reading segment score can be performed according to the existence corresponding to the candidate SV region. On this basis, a unit can be obtained by target scoring, and a target score can be obtained according to the position score and the reading segment score corresponding to the candidate SV region. For example, the sum of the position score and the reading segment score can be used as the target score. In this way, the target SV region can be screened out from each candidate SV region according to the target score corresponding to each candidate SV region through the chromosome structural variation identification submodule. In practical applications, optionally, the above-mentioned scores can be represented by numbers (for example, 234), letters (for example, ABCD) or Chinese characters (for example, excellent, medium, and poor), etc., which can be set according to actual needs and are not specifically limited here.

[0118] The above technical solution, through a scoring method, evaluates the possibility of a candidate SV region being a target SV region from two aspects, namely, position and read segment, thereby achieving rapid and accurate determination of the target SV region.

[0119] On this basis, optionally, the location score obtaining unit includes the following two subunits:

[0120] A position relationship obtaining subunit is used to obtain, for each candidate structural variation region, the window position of each window corresponding to the candidate structural variation region and the band position of the karyotype band on the chromosome, and determine the position relationship between the window position and the band position;

[0121] The position score obtaining subunit is used to determine a target scoring rule from preset position scoring rules for each candidate structural variation region according to the position relationship corresponding to the candidate structural variation region, and obtain a position score based on the target scoring rule.

[0122] The positional relationship may represent the relationship between the window position and the strip position, such as a containment relationship, an intersection relationship, a separation relationship, or a size relationship, which depends on the actual situation and is not specifically limited here. The subunit is obtained through the positional relationship to obtain the positional relationship.

[0123] Further, the location scoring rule can be understood as a preset rule for indicating the location score corresponding to a certain location relationship. The location scoring subunit is obtained through the location scoring, and from each location scoring rule, a target scoring rule corresponding to the location relationship obtained through the location relationship obtaining subunit is screened out, and then the location score can be obtained based on the target scoring rule.

[0124] The above technical solution utilizes the location scoring rules and combines the location relationship to achieve objective determination of the location score.

[0125] Alternatively, the number of chromosomes is two, or the number of chromosomes is one and involves two arms of the chromosome, then: each window corresponding to the candidate SV region includes a first window on one object and a second window on another object, the window position includes a first window position of the first window and a second window position of the second window, the karyotype band includes a first karyotype band on one object and a second karyotype band on another object, the band position includes a first band position of the first karyotype band and a second band position of the second karyotype band, wherein the object is a chromosome or an arm;

[0126] The location score obtaining unit includes the following three subunits:

[0127] A first score obtaining subunit is used to obtain, for each candidate structural variation region, a first window position and a first stripe position corresponding to the candidate structural variation region, and obtain a first score according to the first window position and the first stripe position;

[0128] A second score obtaining subunit is used to obtain, for each candidate structural variation region, a second window position and a second stripe position corresponding to the candidate structural variation region, and obtain a second score according to the second window position and the second stripe position;

[0129] The position score obtaining subunit is used to obtain a position score for each candidate structural variation region according to a first score and a second score corresponding to the candidate structural variation region.

[0130] In other words, when there are two chromosomes, or when there is a chromosome and two arms of the chromosome, there is a window and a karyotype band on each object (i.e., the chromosome or the arm), and thus a subunit can be obtained through a first score, and a first score can be obtained according to a first window position of a first window on one object and a first band position of a first karyotype band, and a subunit can be obtained through a second score, and a second score can be obtained according to a second window position of a second window on another object and a second band position of a second karyotype band, and then a subunit can be obtained through a position score, and a position score can be obtained according to the scores output by the subunits respectively obtained from the above two scores.

[0131] The above technical solution achieves accurate determination of the location score by performing targeted scoring on each object.

[0132] In order to better understand the various technical solutions in the embodiments of the present invention as a whole, the following description will be continued based on the above example (i.e., SV identification of target samples of balanced translocation No. 1 and No. 11).

[0133] 6. Scoring of candidate SV regions:

[0134] The candidate SV region is a combination of two region windows. Here, it is assumed that window 1 (i.e., the first window in the above text) and karyotype band 1 (i.e., the first karyotype band in the above text) are on chromosome 1, and window 2 (i.e., the second window in the above text) and karyotype band 2 (i.e., the second karyotype band in the above text) are on chromosome 11.

[0135] (1) The candidate SV region is further compared with the karyotype results and scored. The specific formula (i.e., position scoring rule) is as follows:

[0136]

[0137] Pos_Score=pos1_Score+pos2_Score.

[0138] Among them, pos1_1 is the starting position of window 1, pos1_2 is the ending position of window 1; band1_1 is the starting position of karyotype band 1, and band1_2 is the ending position of karyotype band 1. Window 1 is compared with karyotype band 1 to obtain the first score of chromosome 1 (pos1_score).

[0139] Similarly, pos2_1 is the starting position of window 2, pos2_2 is the ending position of window 2; band2_1 is the starting position of karyotype band 2, and band2_2 is the ending position of karyotype band 2. Window 2 is compared with karyotype band 2 to obtain the second score (pos2_score) of chromosome 11.

[0140] Then, the sum of pos1_score and pos2_score is used as the position score (Pos_score).

[0141] (2) Look for evidence of reads-pair and / or split-reads supporting the SV in the candidate SV region. If so, score it as 8, otherwise score it as 0, and obtain the read score (Reads_score).

[0142] (3) The final target score Score = Pos_score + Reads_score.

[0143] In this example, for the candidate SV region of chr1:194200001-194600000, chr11:133700001-133900000, its Pos_score compared with the karyotype result is 6, and it is supported by reads-pair / splited-reads, that is, Reads_score=8, then Score=14, which is the candidate SV region with the highest score among all candidate SV regions, and is therefore selected as the target SV region where SV occurs. At this point, SV identification is completed.

[0144] According to the above description, the above examples are all examples of balanced translocation. Next, an example of inversion is given for comparison, so as to better understand the above technical solutions.

[0145] For example, here, the SV identification of the target sample with chromosome 2 inversion is taken as an example, and its karyotype result is inv(2)(q12q24.2). The specific steps related to the above technical solution are as follows (steps 1, 2 and 6 are similar to the above example, and only 3-5 are described here):

[0146] 3. Determination of the genomic position of the karyotype result: According to the karyotype result inv(2)(q12q24.2), it is pre-judged that the SV occurs on the q arm of chr2, and its corresponding genomic position is chr2:93300000-243199373.

[0147] 4. Extract the reads information of chr2:93300000-243199373 from the final bam file formed in 2.2 to form file 2. Slide the window of 200kb and record the barcode ID of each window.

[0148] 5. Read the file in 4 twice, and each window needs to be compared with the remaining windows of chr2 q, which are windows that have not been compared with this window. See the visualization results for Figure 5a and Figure 5b , Figure 5a The horizontal and vertical axes represent any target window of chr2 for comparison, and each point represents two target windows for comparison. The color of the point represents the size of Barcode_overlap_ratio. Figure 5b is Figure 5a On this basis, the merging process of the two regional windows is indicated by a blue box.

[0149] In this example, for the candidate SV region of chr2: 105700001-105900000, 160900001-161100000, Pos_score compared with the karyotype result is 8, and there is no reads-pair / split-reads support, that is, Reads_score=0, then Score=8, which is the candidate SV region with the highest score among all candidate SV regions, and is therefore used as the target SV region where SV occurs. At this point, SV identification is completed.

[0150] On this basis, in order to prove that the above-mentioned technical solutions can improve the sensitivity of SV recognition, two related existing software and the software of this case compiled based on the above-mentioned technical solutions are used here to perform SV recognition on three target samples respectively. The recognition results are shown in the following table. It can be seen that the software of this case can recognize the target SV area that the existing software cannot recognize, that is, it has better sensitivity than the existing software. Moreover, the running time of the software of this case is lower than that of the existing software, which can better match the needs of actual clinical inspection business.

[0151] Table 1 Comparison of SV recognition results and running time of various software

[0152]

[0153]

[0154] Figure 6It is a structural block diagram of another chromosome structural variation identification device provided by an embodiment of the present invention. This embodiment is optimized based on the above-mentioned technical solutions. In this embodiment, optionally, the above-mentioned identification device also includes: a chromosome structural variation typing module; wherein the chromosome structural variation typing module includes a typing information obtaining unit, a quantity counting unit and a carrier chain determination unit; wherein the typing information obtaining unit is used for obtaining the typing information of each shared barcode respectively for the shared barcodes between each window corresponding to the target structural variation region, wherein the typing information is paternal typing or maternal typing; the quantity counting unit is used to count the third number of shared barcodes belonging to paternal typing and the fourth number of shared barcodes belonging to maternal typing according to the typing information; the carrier chain determination unit is used to determine the carrier chain corresponding to the target structural variation region according to the third number and the fourth number, wherein the carrier chain is a paternal chain or a maternal chain. Wherein, the explanation of the terms that are the same or corresponding to the above-mentioned embodiments will not be repeated here.

[0155] For details, see Figure 6 The chromosome structural variation identification device described in this embodiment includes: a genome position acquisition module 40, a barcode information acquisition module 41, a candidate structural variation region determination module 42, a chromosome structural variation identification module 43 and a chromosome structural variation typing module 44; wherein the chromosome structural variation typing module 44 includes a typing information acquisition unit 441, a quantity counting unit 442 and a carrier chain determination unit 443; wherein,

[0156] The genome position acquisition module 40 is used to acquire the genome position of the karyotype result of the target sample for the chromosome structural variation identification for the target sample;

[0157] The barcode information obtaining module 41 is used to slide the window on the chromosome corresponding to the genome position to obtain the barcode information of the barcode corresponding to each window;

[0158] The candidate structural variation region determination module 42 is used to determine the shared barcode ratio for each two target windows in all the windows according to the barcode information corresponding to the two target windows, so as to determine the candidate structural variation region on the chromosome according to the determined shared barcode ratios;

[0159] The chromosome structural variation identification module 43 is used to obtain the window position of each window corresponding to each candidate structural variation region and the band position of the karyotype band on the chromosome for each candidate structural variation region obtained, so as to obtain the target structural variation region on the chromosome according to the window position and band position corresponding to each candidate structural variation region;

[0160] A typing information obtaining unit 441 is used to obtain typing information of each shared barcode between the windows corresponding to the target structural variation region, wherein the typing information is paternal typing or maternal typing;

[0161] The number counting unit 442 is used to count the third number of shared barcodes belonging to the paternal typing and the fourth number of shared barcodes belonging to the maternal typing according to the typing information;

[0162] The carrier chain determining unit 443 is used to determine the carrier chain corresponding to the target structural variation region according to the third number and the fourth number, wherein the carrier chain is the paternal chain or the maternal chain.

[0163] Among them, through the typing information obtaining unit 441, for each shared barcode in the multiple shared barcodes, the typing information of the shared barcode can be obtained. In combination with the application scenarios that may be involved in the embodiments of the present invention, optionally, the typing information can be the paternal typing (i.e., PAT typing) or the maternal typing (i.e., MAT typing).

[0164] Furthermore, after obtaining the typing information corresponding to all the shared barcodes, the number counting unit 442 can count the third number of shared barcodes belonging to the PAT typing in all the shared barcodes based on the typing information. PAT ) and the fourth number of shared barcodes belonging to MAT typing (Barcode MAT ).

[0165] Furthermore, the carrier chain determination unit 443 determines the Barcode obtained above. PAT and Barcode MAT , it can be determined whether the carrier chain corresponding to the target SV region is the father chain (ie, PAT chain) or the mother chain (ie, MAT chain). For example, the quantity ratio Ratio = Barcode PAT / Barcode MAT , the Ratio can characterize the ratio of supporting PAT chain and MAT chain. Then, when the Ratio is greater than or equal to the preset first ratio threshold, the carrying chain is considered to be the PAT chain, that is, the SV occurs in the PAT chain; and when the Ratio is less than or equal to the preset second ratio threshold, the carrying chain is considered to be the MAT chain, that is, the SV occurs in the MAT chain.

[0166] For example, here, the first ratio threshold is 2 and the second ratio threshold is 0.5. For the above-mentioned example of SV identification for target samples of balanced translocation No. 1 and No. 11, chromosome 1: Barcode PAT=8, Barcode MAT =26, Ratio=Barcode PAT / Barcode MAT =8 / 26=0.31<0.5, then the chromosome 1 is judged to have SV on the MAT chain; chromosome 11: Barcode PAT =166, Barcode MAT =2, Ratio = Barcode PAT / Barcode MAT =166 / 2=83>2, then the PAT chain is determined to be the one where the SV occurs on chromosome 11. It should be noted that, in theory, the SVs on the two chromosomes should be on the same chain, but since the typing PAT and MAT are randomly assigned, the calculated SVs may be on different chains.

[0167] Example of SV identification for a target sample with an inversion on chromosome 2, chromosome 2: Barcode PAT =144, Barcode MAT =4, Ratio = Barcode PAT / Barcode MAT =144 / 4=36>2, then it is determined that the SV of chromosome 2 is the PAT chain.

[0168] The technical solution of the embodiment of the present invention can automatically identify the carrier chain corresponding to the target SV region, and subsequent embryo typing can determine whether the carrier parent is a normal chain or an abnormal chain based on the identification result.

[0169] The above specific implementations do not constitute a limitation on the protection scope of the present invention. It should be understood by those skilled in the art that various modifications, combinations, sub-combinations and substitutions can be made according to design requirements and other factors. Any modification, equivalent substitution and improvement made within the spirit and principle of the present invention should be included in the protection scope of the present invention.

Claims

1. A device for identifying chromosome structural variation, characterized in that: include: A genome position acquisition module, for acquiring the genome position of the karyotype result of the target sample for the chromosome structural variation identification, for the target sample to be subjected to the chromosome structural variation identification; A barcode information obtaining module, used for sliding a window on the chromosome corresponding to the genome position to obtain barcode information of the barcode corresponding to each window; a candidate structural variation region determination module, configured to determine, for each two target windows in all the windows, a shared barcode ratio according to the barcode information respectively corresponding to the two target windows, so as to determine the candidate structural variation region on the chromosome according to the determined shared barcode ratios; The chromosome structural variation identification module is used to obtain the window position of each window corresponding to each candidate structural variation region and the band position of the karyotype band on the chromosome for each candidate structural variation region obtained, so as to obtain the target structural variation region on the chromosome according to the window position and band position respectively corresponding to each candidate structural variation region.

2. The device according to claim 1, characterized in that: The candidate structure variation region determination module includes a shared barcode ratio determination submodule and a candidate structure variation region determination submodule; The shared barcode ratio determination submodule is used to determine the shared barcode ratio for every two target windows in all the windows according to the barcode information respectively corresponding to the two target windows; The candidate structural variation region determination submodule is used to determine the candidate structural variation region on the chromosome according to the obtained ratios of all the shared barcodes.

3. The device according to claim 2, characterized in that: The shared barcode ratio determination submodule includes a quantity determination unit and a shared barcode ratio determination unit; The quantity determination unit is used to determine, for every two target windows in all the windows, a first quantity of shared barcodes between the two target windows and a second quantity of different types of barcodes involved in the two target windows according to the barcode information respectively corresponding to the two target windows; The shared barcode ratio determining unit is configured to determine the shared barcode ratio of the shared barcodes according to the first quantity and the second quantity.

4. The device according to claim 2, characterized in that: The candidate structure variation region determination submodule includes a shared barcode ratio filtering unit and a candidate structure variation region determination unit; The shared barcode ratio filtering unit is used to filter all the obtained shared barcode ratios based on a preset ratio threshold to obtain a retained shared barcode ratio; The candidate structural variation region determining unit is used to determine the candidate structural variation region on the chromosome based on the two target windows corresponding to the respective retained shared barcode ratios.

5. The device according to claim 4, characterized in that: The candidate structure variant region determination unit is specifically used to: For each of the obtained retained shared barcode ratios, the two target windows corresponding to the retained shared barcode ratios are respectively used as regional windows; In the case that there are adjacent region windows in positions among all the obtained region windows, merging the adjacent region windows, and updating all the region windows based on the merging result; Based on all of the region windows, candidate structural variation regions on the chromosome are determined.

6. The device according to claim 2, characterized in that: The shared barcode ratio determination submodule is further used for: In the case where there are two chromosomes, each window on one chromosome is paired with each window on another chromosome one by one, and the two paired windows are used as two target windows; In the case where the number of the chromosome is one and the p arm and the q arm of the chromosome are involved, each of the windows on the p arm is paired with each of the windows on the q arm one by one, and the two paired windows are used as the two target windows; When the number of the chromosome is one and the same arm of the chromosome is involved, each window on the arm is paired one by one with each window in all the windows that has not been paired with the window, and the two paired windows are used as the two target windows.

7. The device according to claim 1, characterized in that: The chromosome structural variation recognition module is also used for: The existence of the target reads on the candidate structural variation regions is obtained, so as to obtain the target structural variation regions on the chromosome according to the window positions, band positions and existence conditions respectively corresponding to the candidate structural variation regions, wherein the target reads include read pairs and / or split reads.

8. The device according to claim 7, characterized in that The chromosome structural variation recognition module includes a regional scoring submodule and a chromosome structural variation recognition submodule; wherein the regional scoring submodule includes the following three units: a position score obtaining unit, for obtaining, for each of the candidate structural variation regions, the window position of each of the windows corresponding to the candidate structural variation region and the band position of the karyotype band on the chromosome, and obtaining a position score according to the window position and the band position; a read score obtaining unit, configured to obtain, for each of the candidate structural variation regions, a presence of a target read on the candidate structural variation region, and obtain a read score according to the presence; a target score obtaining unit, configured to obtain a target score for each of the candidate structural variation regions according to a position score and a read score corresponding to the candidate structural variation region; Among them, the chromosome structural variation identification submodule is used to obtain the target structural variation region on the chromosome according to the target score corresponding to each candidate structural variation region.

9. The device according to claim 8, characterized in that The position score obtaining unit includes the following two subunits: a position relationship obtaining subunit, for obtaining, for each of the candidate structural variation regions, the window positions of the windows corresponding to the candidate structural variation region and the band positions of the karyotype bands on the chromosome, and determining the position relationship between the window positions and the band positions; The position score obtaining subunit is used to determine a target scoring rule from preset position scoring rules for each of the candidate structural variation regions according to the positional relationship corresponding to the candidate structural variation regions, and obtain a position score based on the target scoring rule.

10. The device according to claim 8, characterized in that The number of the chromosomes is two, or the number of the chromosome is one and involves two arms of the chromosome, then: Each of the windows includes a first window on an object and a second window on another of the objects, the window positions include a first window position of the first window and a second window position of the second window, and the karyotype bands include a first karyotype band on one of the objects and a second karyotype band on another of the objects, the band positions include a first band position of the first karyotype band and a second band position of the second karyotype band, wherein the object is the chromosome or the arm; The location score obtaining unit includes the following three subunits: a first score obtaining subunit, configured to obtain, for each of the candidate structural variation regions, a first window position and a first stripe position corresponding to the candidate structural variation region, and obtain a first score according to the first window position and the first stripe position; A second score obtaining subunit is used to obtain, for each of the candidate structural variation regions, a second window position and a second stripe position corresponding to the candidate structural variation region, and obtain a second score according to the second window position and the second stripe position; The position score obtaining subunit is used to obtain a position score for each of the candidate structural variation regions according to the first score and the second score corresponding to the candidate structural variation region.

11. The device according to claim 1, characterized in that Also includes: A chromosome structural variation typing module; wherein the chromosome structural variation typing module comprises a typing information obtaining unit, a quantity counting unit and a carrier chain determining unit; wherein, The typing information obtaining unit is used to obtain the typing information of each shared barcode between the windows corresponding to the target structural variation region, wherein the typing information is the paternal typing or the maternal typing; The quantity counting unit is used to count the third quantity of the shared barcodes belonging to the paternal typing and the fourth quantity of the shared barcodes belonging to the maternal typing according to the typing information; The carrier chain determination unit is used to determine the carrier chain corresponding to the target structural variation region according to the third number and the fourth number, wherein the carrier chain is a paternal chain or a maternal chain.

12. The device according to claim 1, characterized in that Also includes: A target file generation module, used to obtain the whole genome sequencing data of the target sample, and compare the whole genome sequencing data with a preset reference genome to generate a target file; Correspondingly, the barcode information obtaining module is specifically used to perform a sliding window on the chromosome corresponding to the genomic position to obtain the barcode information of the barcode corresponding to each window based on the read segment information corresponding to the genomic position extracted from the target file.

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