Method and apparatus for bulk updating genome assembly and annotation file ids

Abstract

The application provides a method and device for batch updating of genome assembly and annotation file IDs. The method comprises the following steps: S1, using mummer software to perform alignment with a reference genome of a known closely related species, and updating the original ID of the genome into a new ID consistent with the order of chromosomes and the order of directions on the reference genome; and S2, using a preset gene naming format to sort the positions of each gene on the corresponding chromosome, so as to obtain an annotation file of the new ID of each gene. The method is simple and fast in batch updating, and the updated ID format is uniform, which is easy for subsequent analysis.

Description

TECHNICAL FIELD

[0001] The present application relates to the field of genome assembly and annotation, and in particular, to a method and device for batch updating genome assembly and annotation file IDs. BACKGROUND

[0002] Genome assembly and annotation are the core of bioinformatics. Genome assembly is to assemble reads generated by sequencing into a genome base sequence. Genome assembly first constructs contigs according to the overlap between sequencing sequences, and then uses allhic and other software to cluster, sort and adjust the direction of contigs to obtain a final chromosome-level genome. The format of the genome is fasta format. Each sequence information in the fasta format file consists of two parts, which are divided into description lines and sequence lines. The description line starts with a greater than sign (>), the content can be filled at will, there is no repetition, and generally stores the ID or name of the sequence. The sequence line is a nucleic acid or protein sequence represented by one or more lines of nucleic acid (ATCG) or amino acid letter abbreviations.

[0003] After the genome assembly is completed, the genome sequence needs to be annotated. Genome annotation mainly includes four aspects: repeat annotation, ncRNA annotation, gene structure annotation and gene function annotation. Before annotation, a gene model is first constructed, and there are three strategies: 1) homology-based prediction: the protein of some genes is highly conserved between similar species, so the existing high-quality annotation information of the close species can be used to determine the exon boundary and splicing site through sequence alignment; 2) transcriptome-based prediction: assisted annotation through RNA-seq data of the species can more accurately determine the exon region and splicing site; 3) de novo prediction: the gene structure is predicted by using the existing probability model. Each method has its own advantages and disadvantages, so the Evidence Modeler (EVM) tool needs to be used for integration in the end, and the complete gene structure is combined. Based on the reliable gene structure, subsequent functional annotation can be carried out. The result of annotation is generally a gff (general feature format) file, and the gff file has a total of 9 columns, which are: (1) sequence ID; (2) sequence source; (3) sequence type; (4) sequence start position; (5) sequence end position; (6) score value; (7) positive and negative chain information; (8) phase information; (9) sequence attribute. According to the gff file, a CDS (coding sequence) file and a protein pep (protein) file will be generated, and the two files are in fasta format.

[0004] After the genome assembly and annotation are completed, the sequence name of the genome and the annotated sequence name will be named according to the fixed id according to the selection of the assembly and annotation software. For example, after the genome mounting is completed using the allhic software, the mounted chromosome id is Hic_asm_01, Hic_asm_02, etc., and after the genome annotation is completed using the evm, the gene sequence id is evm.TU.Hic_asm_01.1, evm.TU.Hic_asm_01.2, etc. In subsequent genome comparison analysis, different id naming methods will make reading confused and not intuitive, so it needs to be converted into a unified naming format.

[0005] However, how to provide a simple and easy-to-read and format-unified genome assembly and annotation file, there is no effective solution at present. SUMMARY

[0006] The main purpose of the present application is to provide a method and device for batch updating the id of the genome assembly and annotation file, so as to solve the problem of non-uniform naming format of different software in the prior art and difficult to accurately read.

[0007] In order to achieve the above object, according to one aspect of the present application, a method for batch updating genome assembly and annotation file ID is provided, which comprises: S1, updating the original ID of the genome to a new ID consistent with the order of the chromosome sequence and the order of the direction on the reference genome of the known closely related species by using the mummer software to align the genome with the reference genome of the known closely related species; S2, obtaining the annotation file of the new ID of each gene by sorting the position of each gene on the corresponding chromosome according to a preset gene naming format.

[0008] Further, S1 comprises: updating the original ID of the chromosome on the genome to a new ID consistent with the order of the chromosome sequence and the order of the direction on the reference genome by using the mummer software to align the genome with the reference genome of the known closely related species, and obtaining a correspondence file of the new ID and the original ID of the chromosome; updating and replacing the ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome.

[0009] Further, the principle of updating and replacing the original ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome comprises: if the direction of the chromosome is reverse, outputting the reverse complementary sequence, and if the direction of the chromosome is forward, the sequence is not processed.

[0010] Further, S2 comprises: presetting the naming format of the gene ID in the annotation file; obtaining a correspondence file of the new ID and the original ID of each gene according to the position of each gene on the chromosome; and replacing the original ID in the annotation file according to the correspondence file of the new ID and the original ID of each gene, thereby obtaining the annotation file with the new ID of each gene.

[0011] Further, the naming format of the gene ID in the annotation file is preset in the following order: the Latin name abbreviation of the species, the chromosome ID, and the position of the gene on the chromosome.

[0012] Further, obtaining the correspondence file of the new ID and the original ID of each gene according to the position of each gene on the chromosome comprises: according to whether the direction of the chromosome is forward or reverse, if the direction of the chromosome is forward, sequentially arranging the original ID of each gene according to the order of each gene on the reference genome, and outputting the correspondence file of the new ID and the original ID of each gene from small to large; and if the direction of the chromosome is reverse, inversely arranging the original ID of each gene according to the order of each gene on the reference genome, and outputting the correspondence file of the new ID and the original ID of each gene from small to large.

[0013] Further, the annotation file includes a structure annotation file and a function annotation file, after obtaining the annotation file with the new gene ID, the method further includes at least one of the following: 1) replacing the transcript ID column in the annotation file with the new ID of the corresponding gene; 2) extracting the CDS sequence of the new gene ID and translating it into a protein sequence.

[0014] Further, the annotation file includes a repeat sequence annotation file and / or an ncRNA annotation file, after obtaining the correspondence file of the new ID and the original ID of the chromosome, the method further includes: replacing the original ID of the chromosome in the repeat sequence annotation file and the ncRNA annotation file with the new ID.

[0015] According to a second aspect of the present application, a device for batch updating genome assembly and annotation file ID is provided, which includes: a chromosome ID updating module and a gene ID updating module, the chromosome ID updating module is configured to use the mummer software to align with the reference genome of the known close relative species, and update the original ID of each chromosome on the genome to the new ID consistent with the order and direction order of the chromosome on the reference genome; the gene ID updating module is configured to sort the position of each gene on the corresponding chromosome by using a preset gene naming format, thereby obtaining an annotation file of the new ID of each gene.

[0016] Further, the chromosome ID updating module includes: an alignment updating unit configured to use the mummer software to align the genome with the reference genome of the known close relative species, update the original ID of the chromosome on the genome to the new ID consistent with the order and direction order of the chromosome on the reference genome, and obtain a correspondence file of the new ID and the original ID of the chromosome; a chromosome ID updating unit configured to update and replace the ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome.

[0017] Further, the chromosome ID updating module unit includes: an output subunit configured to output the reverse complementary sequence when the direction of the chromosome is reverse, and directly output the sequence without any processing when the direction of the chromosome is forward.

[0018] Further, the gene ID updating module includes: a preset module configured to preset the naming format of the gene ID in the annotation file; a correspondence module configured to obtain a correspondence file of the new ID and the original ID of each gene according to the position of each gene on the chromosome; and a gene ID replacing module configured to replace the original ID in the annotation file according to the correspondence file of the new ID and the original ID of each gene, thereby obtaining an annotation file with the new ID of each gene.

[0019] Further, the preset module presets the naming format of the gene ID in the annotation file in the following order: Latin name abbreviation of the species, chromosome ID, and position of the gene on the chromosome.

[0020] Further, the corresponding module comprises: a sequentially arranged output module configured to arrange the original IDs of the genes in sequence according to the order of the genes on the reference genome and output the correspondence file of the new ID and the original ID of the genes in ascending order when the chromosome is forward; and a reversely arranged output module configured to arrange the original IDs of the genes in reverse sequence according to the order of the genes on the reference genome and output the correspondence file of the new ID and the original ID of the genes in ascending order when the chromosome is reverse.

[0021] Further, the annotation file comprises a structural annotation file and a functional annotation file, and the device further comprises at least one of the following: 1) a transcript ID replacement module configured to replace the transcript ID column in the annotation file with the new ID of the corresponding gene; and 2) a CDS translation module configured to extract the CDS sequence of the new ID of the gene and translate it into a protein sequence.

[0022] Further, the annotation file comprises a repeat sequence annotation file and / or an ncRNA annotation file, and the device further comprises: a repeat sequence annotation file ID replacement module configured to replace the original ID of the chromosome in the repeat sequence annotation file with the new ID; and / or an ncRNA annotation file ID replacement module configured to replace the original ID of the chromosome in the ncRNA annotation file with the new ID.

[0023] According to a third aspect of the present application, a computer-readable storage medium is also provided, which comprises a stored program, wherein the program, when executed, controls the device where the storage medium is located to perform any of the above methods for batch updating the IDs of the genome assembly and the annotation file.

[0024] According to a fourth aspect of the present application, a processor is also provided, which is configured to execute a program, wherein the program, when executed, performs any of the above methods for batch updating the IDs of the genome assembly and the annotation file.

[0025] By comparing with the reference genome of the proximal species to obtain the correspondence file of the new ID and the original ID of the chromosome, the technical solution of the present application facilitates updating the IDs of the chromosomes. The naming format of the genes is preset according to actual needs, and the naming format is simple and easy to understand, which facilitates subsequent analysis. The original IDs of the genes in the annotation file are updated to the new IDs. The updating method is simple and fast, batch processing, and the updated ID format is uniform, which is easy for subsequent analysis. BRIEF DESCRIPTION OF DRAWINGS

[0026] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate an implementation of the application and, together with the description, serve to explain the application. In the drawings,

[0027] Figure 1 A flowchart illustrating a method for batch updating genome and annotation file IDs according to an embodiment of the application is shown. DETAILED DESCRIPTION

[0028] It should be noted that the embodiments in the present application and the features in the embodiments can be combined with each other without conflict. The present application will be described in detail below with reference to the embodiments.

[0029] As mentioned in the background section, after the existing genome assembly and annotation are completed, different assembly and annotation software will have different chromosome and gene ID names, and the chromosome number order is random. In order to facilitate comparison with closely related species genomes and subsequent analysis drawing, the chromosome ID of the target species genome needs to be modified by referring to the chromosome order and direction of the published closely related species. However, there is currently no effective solution to provide a simple and easy-to-read and uniform format genome assembly and annotation file. In order to improve this situation and to further more intuitively display the gene information of the species annotation, it is generally required to name the geneID with the Latin name abbreviation of the species, the chromosome ID and the position order of the gene on the chromosome. The inventors of the present application provide a method and process for batch updating genome and annotation file IDs, which can uniformly name the sequence ID of the genome sequence and the annotation sequence. The present application can batch modify the chromosome ID to Chr01, Chr02, etc., and modify the gene name to 01G0001, 01G0002, etc. The naming format is simple and easy to understand, and is convenient for subsequent analysis. On this basis, the applicant proposes a series of protection schemes of the present application.

[0030] In a first typical embodiment of the present application, the present application provides a method for batch updating genome and annotation file IDs, the method comprising: S1, using the mummer software to align with the reference genome of the known closely related species, updating the original ID of the genome to the new ID consistent with the chromosome order and direction order on the reference genome; S2, using a preset gene naming format to sort the position of each gene on the corresponding chromosome, thereby obtaining an annotation file of the new ID of each gene.

[0031] The above embodiments of the present application obtain the correspondence file of the new ID and the original ID of the chromosome by aligning with the reference genome of the closely related species, and then update the chromosome ID. The gene naming format is preset according to the actual needs, and the naming format is simple and easy to understand, which is convenient for subsequent analysis. Then, the original ID of the gene in the annotation file is updated to the new ID according to the preset format. The updating method is simple, fast, batch and easy for subsequent analysis.

[0032] In order to facilitate the comparison with the genome of the closely related species and the subsequent analysis drawing, it is usually necessary to refer to the chromosome order and direction of the published closely related species to modify the chromosome ID of the target species genome. In order to further improve the speed and quantity of chromosome updating, in a preferred embodiment, S1 includes: using mummer software to align the genome with the reference genome of the known closely related species, updating the original ID of the chromosome on the genome to the new ID consistent with the order and direction of the chromosome on the reference genome, and obtaining the correspondence file of the new ID and the original ID of the chromosome; updating and replacing the ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome.

[0033] In order to further ensure the accuracy of the updated chromosome ID, it is necessary to ensure the correct direction of the chromosome. In a preferred embodiment, the principle of updating and replacing the original ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome includes: if the direction of the chromosome is reverse, output the reverse complementary sequence, if it is forward, the sequence is not processed.

[0034] In a preferred embodiment, S2 includes: presetting the naming format of the gene ID in the annotation file; obtaining the correspondence file of the new ID and the original ID of each gene according to the position sequence of each gene on the chromosome; replacing the original ID in the annotation file according to the correspondence file of the new ID and the original ID of each gene, thereby obtaining the annotation file with the new ID of each gene.

[0035] In a preferred embodiment, the naming format of the gene ID in the annotation file is preset in the following order: Latin name abbreviation of the species, chromosome ID and position sequence of the gene on the chromosome.

[0036] In order to more conveniently compare the genome annotation with the closely related species, the above preferred embodiment develops the above new genome naming format unified method by referring to the naming format of the genome of the model species Arabidopsis thaliana, thereby making the gene ID information more simple and easy to read.

[0037] The above preferred embodiments of the present application can uniformly format the names of the genomic sequence and the annotated sequence ID, and can batch modify the chromosome ID to Chr01, Chr02, etc., and modify the gene name to 01G0001, 01G0002, etc.

[0038] To further improve the accuracy of the updated gene ID, in a preferred embodiment, the obtaining of the correspondence file of the new ID and the original ID of the gene according to the position of each gene on the chromosome includes: according to whether the direction of the chromosome is forward or reverse, if the chromosome is forward, arranging the original IDs of the genes in order according to the order of the genes on the reference genome, and outputting the correspondence file of the new ID and the original ID of the gene from small to large; if the chromosome is reverse, arranging the original IDs of the genes in reverse order according to the order of the genes on the reference genome, and outputting the correspondence file of the new ID and the original ID of the gene from small to large.

[0039] The genomic annotation mainly includes four aspects: repeat annotation, ncRNA annotation, gene structure annotation, and gene function annotation. Therefore, after obtaining the correspondence file of the new ID and the original ID of the gene, the IDs in the files related to the gene structure annotation and the gene function annotation need to be updated. Therefore, in a preferred embodiment, the annotation file includes a structure annotation file and a function annotation file, and after obtaining the annotation file with the new ID of the gene, the method further includes at least one of the following: 1) replacing the transcript ID column in the annotation file with the new ID of the corresponding gene; 2) extracting the CDS sequence of the new ID of the gene and translating it into a protein sequence. In another preferred embodiment, the annotation file includes a repeat sequence annotation file and / or an ncRNA annotation file, and after obtaining the correspondence file of the new ID and the original ID of the chromosome, the method further includes: replacing the original ID of the chromosome in the repeat sequence annotation file and the ncRNA annotation file with the new ID.

[0040] After the above steps, the rapid batch updating of the genomic and annotation file ID of the present application can be realized, and the genomic and annotation file after ID updating is easier for subsequent analysis.

[0041] The beneficial effects of the present application will be further explained in detail below with specific embodiments.

[0042] Embodiment 2

[0043] This embodiment provides a method for batch updating the genomic and annotation file ID, and the specific process is as shown in Figure 1 The method includes the following steps:

[0044] 1) Obtain the chromosome correspondence: the target species genome and the published reference genome are aligned using mummer software to obtain the chromosome ordering and direction correspondence.

[0045] 2) Modify the genome file: modify and replace the ID of the genome according to the correspondence between the new and old IDs of the chromosomes. If the direction is reverse, output the reverse complementary sequence. If it is forward, the sequence is not processed.

[0046] 3) Modify the gene gff file: determine the naming format of the modified gene and transcript ID, output the correspondence between the new and old IDs according to the position of the gene on the chromosome, and arrange the new and old correspondence according to the chromosome direction. If the chromosome is forward, arrange the ID from small to large according to the genome coordinate sequence. If the chromosome is reverse, arrange the ID from small to large according to the reverse coordinate sequence; replace the ID in the gff file according to the new and old correspondence, and finally obtain the new gff file.

[0047] 4) Extract the cds sequence of the new ID and translate it into protein sequence: according to the modified genome and the modified gff file, extract the cds sequence of the new ID, and then translate it into the corresponding protein sequence.

[0048] 5) Modify the transcript ID of the functional annotation text file: replace the transcript ID column in the functional annotation result file with the corresponding new ID.

[0049] 6) Modify the gff file in the repeat sequence annotation: modify the chromosome ID in the repeat sequence annotation result gff file according to the correspondence between the new and old IDs of the chromosomes. If the correspondence is forward, only modify the ID. If it is negative, the corresponding position on the chromosome also needs to be modified.

[0050] 7) Modify the ncRNA annotation file: same as 6).

[0051] Example 3

[0052] The following is an example of the partial modification results of soybean genome and annotation file. The modification of the annotation file of this species takes 5 minutes.

[0053]

[0054] In the collinearity analysis, the genes of the two genomes can be used to obtain the collinearity of the gene block by Mcscan.

[0055] It should be noted that, for the aforementioned method embodiments, the series of acts combined for a simple description, but those skilled in the art should know that the present application is not limited to the described sequence of acts, because according to the present application, some steps can be performed in other sequences or simultaneously. Secondly, those skilled in the art should know that the embodiments described in the specification are all preferred embodiments, and the acts involved are not necessarily essential to the present application.

[0056] From the above description of the embodiments, those skilled in the art can clearly understand that the present application can be implemented by means of software and necessary detection instruments and other hardware devices. Based on such understanding, the data processing part of the technical solutions of the present application can be embodied in the form of a software product, which can be stored in a storage medium, such as ROM / RAM, magnetic disk, optical disk, etc., including a number of instructions to make a computer device (which can be a personal computer, server, or network device, etc.) execute the methods of various embodiments or some parts of the embodiments of the present application.

[0057] The present application can be used in many general or special-purpose computing 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 electronics, network PCs, minicomputers, mainframe computers, distributed computing environments including any of the above systems or devices, etc.

[0058] Obviously, those skilled in the art should understand that some modules or steps of the present application described above can be implemented on a general computing device, which can be concentrated on a single computing device, or distributed on a network composed of multiple computing devices, and optionally, they can be implemented by program codes executable by a computing device, so that they can be stored in a storage device and executed by a computing device, or they can be made into individual integrated circuit modules, or multiple modules or steps among them can be made into a single integrated circuit module to implement. Thus, the present application is not limited to any specific combination of hardware and software.

[0059] Example 4

[0060] The embodiment provides a device for batch updating genome assembly and annotation file IDs, which comprises a chromosome ID updating module and a gene ID updating module, wherein the chromosome ID updating module is configured to update original IDs of chromosomes on a genome to new IDs consistent with chromosome order and direction order on a reference genome of a known closely related species by using a mummer software to perform alignment on the genome and the reference genome; and the gene ID updating module is configured to obtain an annotation file of new IDs of genes by sorting positions of the genes on corresponding chromosomes according to a preset gene naming format.

[0061] Optionally, the chromosome ID updating module comprises an alignment updating unit configured to update original IDs of chromosomes on a genome to new IDs consistent with chromosome order and direction order on a reference genome of a known closely related species by using a mummer software to perform alignment on the genome and the reference genome, and obtain a correspondence file of the new IDs and the original IDs of the chromosomes.

[0062] Optionally, the chromosome ID updating unit comprises an output subunit configured to output a reverse complementary sequence when the direction of a chromosome is reverse, and directly output the sequence without any processing when the direction of the chromosome is forward.

[0063] Optionally, the gene ID updating module comprises a preset module configured to preset a naming format of gene IDs in an annotation file, a correspondence module configured to obtain a correspondence file of new IDs and original IDs of genes according to position sorting of the genes on chromosomes, and a gene ID replacing module configured to replace the original IDs in the annotation file according to the correspondence file of the new IDs and the original IDs of the genes, so as to obtain the annotation file with the new IDs of the genes.

[0064] Optionally, the preset module presets the naming format of the gene IDs in the annotation file in the following order: a Latin name abbreviation of a species, a chromosome ID, and position sorting of the genes on the chromosome.

[0065] Optionally, the correspondence module comprises a sequence arrangement output module and a reverse sequence arrangement output module, wherein the sequence arrangement output module is configured to arrange original IDs of genes in sequence according to the order of the genes on a reference genome when the direction of a chromosome is forward, and output a correspondence file of new IDs and the original IDs of the genes from small to large; and the reverse sequence arrangement output module is configured to arrange the original IDs of the genes in reverse sequence according to the order of the genes on the reference genome when the direction of the chromosome is reverse, and output the correspondence file of the new IDs and the original IDs of the genes from small to large.

[0066] Optionally, the annotation file comprises a structure annotation file and a function annotation file, and the device further comprises at least one of the following: 1) a transcript ID replacement module configured to replace a transcript ID column in the annotation file with a new ID of a corresponding gene; and 2) a CDS translation module configured to extract a CDS sequence of the new ID of the gene and translate the CDS sequence into a protein sequence.

[0067] Optionally, the annotation file comprises a repeat sequence annotation file and / or an ncRNA annotation file, and the device further comprises: a repeat sequence annotation file ID replacement module configured to replace a previous ID of a chromosome in the repeat sequence annotation file with a new ID; and / or an ncRNA annotation file ID replacement module configured to replace a previous ID of a chromosome in the ncRNA annotation file with a new ID.

[0068] Embodiment 5

[0069] The embodiment provides a computer-readable storage medium, which comprises a stored program, wherein the program, when executed, controls a device where the storage medium is located to perform any of the above methods for batch updating IDs of a genome assembly and an annotation file.

[0070] The embodiment also provides a processor for executing a program, wherein the program, when executed, performs any of the above methods for batch updating IDs of a genome assembly and an annotation file.

[0071] From the above description, it can be seen that the above embodiments of the present application achieve the following technical effects:

[0072] (1) The present application uses mummer and a reference genome for alignment, so that the changed ID is consistent with the published reference genome order.

[0073] (2) The gene naming rule of the present application is to sort according to the physical position on the chromosome from large to small, and the species Latin abbreviation is added in the ID name. Only from the ID naming, the species information of the gene, the chromosome number where the gene is located, and the position of the gene on the chromosome are intuitively displayed, which facilitates later analysis, such as the duplication mode of a certain gene family, whether a certain metabolic pathway gene exists in clusters, identification of polyploid alleles, etc.

[0074] (3) Simple operation: only 4 parameters in the process need to be modified, i.e. species abbreviation, input file path, result output path, and file prefix, and the modified genome and annotation result file can be obtained.

[0075] (4) Fast operation: the present application can quickly modify the ID name of the genome and the annotation result file in batches. The modification of the genome ID of a 1G genome can be completed within half an hour, and the modification of the annotation result file can be completed within 5 minutes.

[0076] The above description is only the preferred embodiment of the present application, and is not intended to limit the present application. The present application can have various changes and modifications for those skilled in the art. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present application shall be included in the protection scope of the present application.

Claims

1. A method of bulk updating genomic assembly and annotation file IDs, characterized in that, The method comprises: S1, using mummer software to align with the reference genome of known closely related species, updating the original ID of the chromosome on the genome to a new ID consistent with the order of the chromosome sequence and the order of the direction on the reference genome, to obtain a correspondence file of the new ID and the original ID of the chromosome; According to the correspondence file of the new ID and the original ID of the chromosome, the ID of each chromosome on the genome is updated and replaced; If the direction of the chromosome is reverse, the reverse complementary sequence is output, and if it is forward, the sequence is not processed; S2, using a preset gene naming format to sort the position of each gene on the corresponding chromosome, thereby obtaining an annotation file of each gene new ID; The naming format of the gene ID in the preset annotation file; According to the position sorting of each gene on the chromosome, a correspondence file of the new ID and the original ID of each gene is obtained; According to the correspondence file of the new ID and the original ID of each gene, the original ID in the annotation file is replaced, thereby obtaining an annotation file with each gene new ID; The naming format of the gene ID in the annotation file is preset in the following order: Latin name abbreviation of the species, chromosome ID, and position sorting of the gene on the chromosome; According to the position sorting of each gene on the chromosome, a correspondence file of the new ID and the original ID of each gene is obtained, comprising: If the direction of the chromosome is forward, the original ID of each gene is sequentially arranged according to the order of each gene on the reference genome, and the correspondence file of the new ID and the original ID of each gene is output from small to large; If the chromosome is reverse, the original ID of each gene is inversely arranged according to the order of each gene on the reference genome, and the correspondence file of the new ID and the original ID of each gene is output from small to large.

2. The method of claim 1, wherein, The annotation file includes structural annotation file and functional annotation file, after obtaining the annotation file with gene new ID, the method further comprises at least one of the following: 1) replacing the transcript ID column in the annotation file with the new ID of the corresponding gene; 2) extracting the CDS sequence of the gene new ID and translating it into a protein sequence.

3. The method of claim 2, wherein, The annotation file includes repeat sequence annotation file and / or ncRNA annotation file, after obtaining the correspondence file of the new ID and the original ID of the chromosome, the method further comprises: replacing the original ID of the chromosome in the repeat sequence annotation file and the ncRNA annotation file with the new ID.

4. An apparatus for batch updating genome assembly and annotation file IDs, characterized in that, The device comprises: A chromosome ID updating module is configured to use mummer software to align with the reference genome of known closely related species, and update the original ID of each chromosome on the genome to a new ID consistent with the order of the chromosome sequence and the order of the direction on the reference genome; A gene ID updating module is configured to use a preset gene naming format to sort the position of each gene on the corresponding chromosome, thereby obtaining an annotation file of each gene new ID; The gene ID updating module comprises: A preset module is configured to preset the naming format of the gene ID in the annotation file; The naming format of the gene ID in the preset annotation file; The correspondence module is configured to obtain a correspondence file of the new ID and the original ID of each gene according to the positions of the genes on the chromosomes; The chromosome ID updating module comprises: The alignment updating unit is configured to use the mummer software to align the genome with the reference genome of the known closely related species, update the original ID of the chromosome on the genome to the new ID consistent with the order and direction order of the chromosome on the reference genome, and obtain a correspondence file of the new ID and the original ID of the chromosome; The chromosome ID updating unit is configured to update and replace the ID of each chromosome on the genome according to the correspondence file of the new ID and the original ID of the chromosome; The chromosome ID updating module comprises: The output subunit is configured to output the reverse complementary sequence when the direction of the chromosome is reverse, and directly output the sequence without any processing when the direction of the chromosome is forward. The gene ID replacing module is configured to replace the original ID in the annotation file according to the correspondence file of the new ID and the original ID of each gene, so as to obtain an annotation file with the new ID of each gene. The preset module presets the naming format of the gene ID in the annotation file in the following order: Latin name abbreviation of the species, chromosome ID, and position of the gene on the chromosome; The correspondence module comprises: The order arrangement output module is configured to arrange the original ID of each gene in order according to the order of each gene on the reference genome when the direction of the chromosome is forward, and output the correspondence file of the new ID and the original ID of the gene from small to large. The reverse order arrangement output module is configured to arrange the original ID of each gene in reverse order according to the order of each gene on the reference genome when the direction of the chromosome is reverse, and output the correspondence file of the new ID and the original ID of the gene from small to large.

5. The apparatus of claim 4, wherein, The annotation file comprises a structural annotation file and a functional annotation file, and the device further comprises at least one of the following: 1) The transcript ID replacing module is configured to replace the transcript ID column in the annotation file with the new ID of the corresponding gene. 2) The CDS translation module is configured to extract the CDS sequence of the new ID of the gene and translate it into a protein sequence.

6. The apparatus of claim 5, wherein, The annotation file comprises a repeat sequence annotation file and / or an ncRNA annotation file, and the device further comprises: The repeat sequence annotation file ID replacing module is configured to replace the original ID of the chromosome in the repeat sequence annotation file with the new ID; and / or The ncRNA annotation file ID replacing module is configured to replace the original ID of the chromosome in the ncRNA annotation file with the new ID.

7. A computer readable storage medium characterized in that, The computer readable storage medium comprises a stored program, wherein the program controls the device where the storage medium executes the method for batch updating the genome assembly and the annotation file ID according to any one of claims 1 to 3 when the program is running.

8. A processor, comprising: The processor is configured to run a program, wherein the program executes the method for batch updating the genome assembly and the annotation file ID according to any one of claims 1 to 3 when the program is running.

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