Method and device for evaluating the annotation quality of genome

Abstract

The present invention provides a method and device for evaluating the annotation quality of a genome. The method includes: performing single-copy orthologous gene integrity analysis, gene function annotation, expression analysis and gene structure analysis on each gene in the genome to be evaluated for quality, and obtaining an analysis result file; performing quantitative scoring on the analysis result file, and judging the annotation quality of the genome to be evaluated for quality based on the scoring result, and being able to perform multi-dimensional quality evaluation on each gene in the genome in terms of gene integrity, function annotation, expression and gene structure, and making a more comprehensive and accurate judgment on the annotation quality of the genome, which is of great significance for the reliability and applicability evaluation of genome data.

Description

Technical Field

[0001] The present invention relates to the technical field of genomics, and in particular to a method and device for evaluating the annotation quality of a genome. Background Art

[0002] With the development of high-throughput sequencing technology, the genomes of more and more species have been sequenced and published. Genome annotation is the basis of biological research, and a high-quality genome annotation result is of great value to biological research based on the genome.

[0003] Gene set prediction for assembled genomes is an important aspect of genome annotation. Generally speaking, the evidence for gene set prediction in a genome comes from the following three aspects: annotation of gene structure based on transcript sequences, annotation of gene structure based on homologous protein sequences, and de novo prediction of gene structure by software. The final gene set information can be obtained by integrating the three types of evidence. BUSCO (Benchmarking Universal Single-Copy Orthologs) collects conserved sequences between similar species and constructs gene sets of six major phylogenetic branches (Bacteria, Eukaryota, Protists, Metazoa, Fungi, and Plants) using the OrthoDB orthologous database, which can evaluate the completeness of the gene set of genome annotation. In order to evaluate the quality of genome annotation, researchers usually use BUSCO to evaluate the completeness of genome annotation. However, BUSCO can only evaluate the conserved genes in the orthologous database, which are limited in number and cannot fully represent the overall gene set.

[0004] Therefore, how to provide a more accurate and comprehensive scoring and evaluation system for the gene set annotated by the genome, so as to systematically evaluate the quality of the annotated gene set, is of great significance for the subsequent analysis and application of the genome. Summary of the invention

[0005] The main purpose of the present invention is to provide a method and device for evaluating the annotation quality of a genome, so as to solve the problem that the prior art cannot comprehensively and accurately evaluate the annotation quality of a genome.

[0006] In order to achieve the above-mentioned purpose, according to a first aspect of the present invention, a method for evaluating the annotation quality of a genome is provided, the method comprising: performing single-copy orthologous gene integrity analysis, gene function annotation, expression level analysis and gene structure analysis on each gene in the genome to be evaluated, to obtain an analysis result file; performing quantitative scoring on the analysis result file, and judging the annotation quality of the genome to be evaluated based on the scoring result.

[0007] Furthermore, the genome to be assessed for quality is analyzed for single copy orthologous gene integrity using BUSCO software or compleasm software; preferably, the embryophyta_odb10 library in BUSCO software is used for single copy orthologous gene integrity analysis; preferably, gene function annotation is performed using at least one of the following databases: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG.

[0008] Furthermore, performing expression analysis on the genome to be evaluated for quality includes: using hisat2 software to compare each gene in the genome to be evaluated for quality with a reference second-generation transcript, and then using htseq software to convert the comparison result into an expression result of each gene; preferably, performing gene structure analysis on the genome to be evaluated for quality includes: analyzing whether there is a frameshift mutation in the gene in the genome, whether the number of bases in the CDS is an integer multiple of 3, and whether there is a correct start codon and a correct stop codon.

[0009] Furthermore, the criteria for quantitative scoring of the analysis result files are as follows: if the result of the gene to be evaluated by the BUSCO software is Completed or Duplicated, the score is 100 points, if it is Fragmented, the score is 50 points, otherwise no score; if the sum of the expression levels of the genes to be evaluated is greater than 1, the score is 100 points, otherwise no score; if the gene to be evaluated has functional annotation data in 3 or more databases, the score is 100 points, if the number of databases is 2, the score is 95 points, if the number of databases is 1, the score is 90 points; if the gene to be evaluated has a frameshift mutation, no score is given, If there is no frameshift mutation but no correct start codon and / or correct stop codon, the score is increased by 1 point; if there is no frameshift mutation and both the start codon and the stop codon are correct, the score is increased by 2 points; the average of the scores of all genes to be quality assessed in the genome is taken as the final score of the genome to be quality assessed, and the annotation quality of the genome to be quality assessed is judged based on the final score; if the final score is ≥90 points, the annotation quality of the genome to be quality assessed is excellent; if the final score is ≥60 and <90 points, the annotation quality of the genome to be quality assessed is good; if the final score is <60 points, the annotation quality of the genome to be quality assessed is unqualified; the score shall not exceed 100 points.

[0010] In order to achieve the above-mentioned purpose, according to a second aspect of the present invention, there is provided a device for evaluating the annotation quality of a genome, the device comprising: an analysis module, configured to perform single-copy orthologous gene integrity analysis, gene function annotation, expression analysis and gene structure analysis on each gene in the genome to be evaluated for quality, to obtain an analysis result file; and a judgment module, configured to perform quantitative scoring on the analysis result file, and to judge the annotation quality of the genome to be evaluated for quality based on the scoring result.

[0011] Further, the analysis module includes: a gene integrity analysis unit, which is configured to perform single copy orthologous gene integrity analysis on the genome to be assessed for quality using BUSCO software or compleasm software; preferably, the gene integrity analysis unit also includes: a unit configured to perform single copy orthologous gene integrity analysis using the embryophyta_odb10 library in the BUSCO software; preferably, the analysis module also includes: a gene function annotation unit, which is configured to perform gene function annotation using at least one of the following databases: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG.

[0012] Furthermore, the analysis module also includes: an expression analysis unit, which is configured to use the hisat2 software to compare each gene in the genome to be quality assessed with the reference second-generation transcript, and then use the htseq software to convert the comparison result into the expression result of each gene; preferably, the analysis module also includes: a gene structure analysis unit, which is configured to analyze whether there is a frameshift mutation in the gene in the genome, whether the number of bases in the CDS is an integer multiple of 3, and whether there is a correct start codon and a correct stop codon.

[0013] Furthermore, the judgment module includes: a scoring unit, which is configured such that if the result of the gene to be quality evaluated is Completed or Duplicated after evaluation by the BUSCO software, the score output is 100 points, if it is Fragmented, the score output is 50 points, otherwise no score is given; if the sum of the expression levels of the genes to be quality evaluated is greater than 1, the score output is 100 points, otherwise no score is given; if the gene to be quality evaluated has functional annotation data in 3 or more databases, the score output is 100 points, if the number of databases is 2, the score output is 95 points, if the number of databases is 1, the score output is 90 points; if the gene to be quality evaluated has a frameshift mutation, no score is given, and if there is no frameshift mutation, no score is given. mutation, but there is no correct start codon and / or correct stop codon, the score output is increased by 1 point; if there is no frameshift mutation and the start codon and the stop codon are correct, the score output is increased by 2 points; the output result unit is set to take the median of the scores of all genes to be quality assessed in the genome as the final score of the genome to be quality assessed, and use the final score to judge the annotation quality of the genome to be quality assessed; if the final score is ≥90 points, the annotation quality of the genome to be quality assessed is excellent; if the final score is ≥60 and <90 points, the annotation quality of the genome to be quality assessed is good; if the final score is <60 points, the annotation quality of the genome to be quality assessed is unqualified; wherein, the score does not exceed 100 points.

[0014] In order to achieve the above-mentioned object, according to a third aspect of the present invention, a computer-readable storage medium is provided, the storage medium comprising a stored program, wherein when the program is executed, the device where the storage medium is located is controlled to execute the above-mentioned method for evaluating the annotation quality of a genome.

[0015] In order to achieve the above object, according to a fourth aspect of the present invention, a processor is provided, the processor being used to run a program, wherein the program runs the above method for evaluating the annotation quality of a genome.

[0016] By applying the technical solution of the present invention, it is possible to perform a multi-dimensional quality evaluation on each gene in the genome in four aspects: gene integrity, functional annotation, expression level and gene structure, and to make a more accurate judgment on the annotation quality of the genome in a more comprehensive manner, which is of great significance for the reliability and applicability evaluation of genome data. DETAILED DESCRIPTION

[0017] It should be noted that, in the absence of conflict, the embodiments and features in the embodiments of the present application can be combined with each other. The present invention will be described in detail below in conjunction with the embodiments.

[0018] As mentioned in the background technology, the evaluation of gene annotation in the prior art is usually performed using BUSCO, but since BUSCO can only evaluate the conserved genes in the orthologous database, the number is limited and it cannot annotate the entire gene set. Therefore, the present application intends to provide a method that can more comprehensively evaluate the annotation quality of the genome.

[0019] In a first typical embodiment of the present application, a method for evaluating the annotation quality of a genome is provided, the method comprising: performing single copy orthologous gene integrity analysis, gene function annotation, expression analysis, and gene structure analysis on each gene in the genome to be evaluated for quality, and obtaining an analysis result file; performing quantitative scoring on the analysis result file, and judging the annotation quality of the genome to be evaluated for quality by the scoring result. The present application performs annotation analysis on genes from different aspects of gene quality or characteristics, and evaluates the annotation quality of the genome by the annotation analysis results, so as to obtain a relatively accurate and comprehensive evaluation result.

[0020] Any software capable of analyzing gene integrity is applicable to the present application. In order to further obtain more accurate single-copy orthologous gene integrity analysis results, in a preferred embodiment, BUSCO software or compleasm software is used to perform single-copy orthologous gene integrity analysis on the genome to be assessed for quality; preferably, the embryophyta_odb10 library in the BUSCO software is used to perform single-copy orthologous gene integrity analysis.

[0021] Among them, BUSCO software and compleasm software are tools for evaluating genome assembly and annotation integrity. They can evaluate whether the annotated gene set has fully annotated highly conserved single-copy orthologous genes in the database. It is generally believed that if highly conserved single-copy genes can be fully annotated, then the integrity of the gene set annotation is relatively high. Compared with BUSCO software, Compleasm software replaces the core protein-to-genome alignment algorithm, which is faster and more sensitive.

[0022] Any database that can annotate gene function is applicable to the present application. In a preferred embodiment, at least one of the following databases is used for gene function annotation: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG. The URLs of the databases are: SwissProt (https: / / web.expasy.org / docs / swiss-prot_guideline.html), which contains information on protein function, biological process, molecular function, cellular localization, protein family classification, biological pathway and protein structure of genes; NT (https: / / www.ncbi.nlm.nih.gov / nucleotide / ), which contains a large amount of nucleotide sequence information; NR (ftp: / / ftp.ncbi.nlm.nih.gov / blast / db / FASTA / nr.gz), which is a non- Redundant protein sequence database, which provides a collection of deduplicated protein sequences; PFAM (http: / / xfam.org / ), which contains information on protein functions and evolutionary relationships; eggNOG (http: / / eggnogdb.embl.de / ), which contains information on protein phylogeny and function; GO (http: / / geneontology.org / page / go-database), which contains information on molecular functions, cellular components and biological processes; KEGG (http: / / www.genome.jp / kegg / ), which contains information on the functions and interactions of biological molecules in cells.

[0023] Any method capable of analyzing gene expression and gene structure is applicable to the present application. In a preferred embodiment, expression analysis of the genome to be evaluated for quality includes: using hisat2 software to compare each gene in the genome to be evaluated for quality with a reference second-generation transcript, and then using htseq software to convert the comparison result into the expression result of each gene; preferably, gene structure analysis of the genome to be evaluated for quality includes: analyzing whether there is a frameshift mutation in the gene in the genome, whether the number of bases in CDS is an integer multiple of 3 (not triplicate), and whether there is a correct start codon and a correct stop codon.

[0024] Among them, FPKM value (Fragments Per Kilobase of transcript per Million fragments) is an indicator used to measure the gene expression level in RNA sequencing (RNA-Seq) data. It takes into account the effects of sequencing depth and transcript length, so that the gene expression levels between different samples can be compared. The calculation formula of FPKM is (C × 10 3 ) / (N × L); where C is the number of sequenced fragments (Reads) of the gene, N is the sequencing depth (i.e., the total number of sequenced fragments of the gene), and L is the length of the gene (in kilobase pairs, kb). In addition, there are many software that can be used to calculate FPKM to obtain FPKM values, including: RSEM, Kallisto, FeatureCounts, StringTie, etc. This application uses htseq software to convert the alignment results into the number of Reads of the gene, and uses the Reads number to calculate the above FPKM formula to obtain the expression results of each gene.

[0025] In order to quantify the above analysis results into an evaluation index that can be objectively evaluated, in a preferred embodiment, if the result of the gene to be evaluated by the BUSCO software is Completed or Duplicated, the score is 100 points, if it is Fragmented, the score is 50 points, otherwise no score; if the sum of the expression levels of the genes to be evaluated is greater than 1, the score is 100 points, otherwise no score; if the gene to be evaluated has functional annotation data in 3 or more databases, the score is 100 points, if the number of databases is 2, the score is 95 points, and if the number of databases is 1, the score is 90 points; if the gene to be evaluated has a frameshift mutation, no score is given, if there is no frameshift mutation, but there is no correct start codon and / or correct stop codon, the score is increased by 1 point, if there is no frameshift mutation and the start codon and stop codon are correct, the score is increased by 2 points.

[0026] In order to accurately and observably associate the above analysis results with the annotation quality of the genome, in a preferred embodiment, the median of the scores of all genes to be quality assessed in the genome is used as the final score of the genome to be quality assessed, and the annotation quality of the genome to be quality assessed is judged based on the final score; if the final score is ≥90 points, the annotation quality of the genome to be quality assessed is excellent; if the final score is ≥60 and <90 points, the annotation quality of the genome to be quality assessed is good; if the final score is <60 points, the annotation quality of the genome to be quality assessed is unqualified; wherein, the score does not exceed 100 points.

[0027] In a second typical embodiment of the present application, a device for evaluating the annotation quality of a genome is provided, the device comprising: an analysis module, configured to perform single copy orthologous gene integrity analysis, gene function annotation, expression analysis and gene structure analysis on each gene in the genome to be evaluated for quality, and obtain an analysis result file; a judgment module, configured to perform quantitative scoring on the analysis result file, and to judge the annotation quality of the genome to be evaluated for quality based on the scoring result. The present application uses the above-mentioned device to perform annotation analysis on genes from different aspects of gene quality or characteristics, and evaluates the annotation quality of the genome based on the annotation analysis results, so as to obtain a more accurate and comprehensive evaluation result.

[0028] Any software capable of analyzing gene integrity is applicable to the present application. In order to further obtain more accurate single-copy orthologous gene integrity analysis results, in a preferred embodiment, the analysis module includes: a gene integrity analysis unit, which is configured to use BUSCO software or compleasm software to perform single-copy orthologous gene integrity analysis on the genome to be assessed for quality; preferably, the gene integrity analysis unit also includes: a software configured to use the embryophyta_odb10 library in the BUSCO software to perform single-copy orthologous gene integrity analysis; any database capable of annotating gene function is applicable to the present application. In a preferred embodiment, the analysis module also includes: a gene function annotation unit, which is configured to use at least one of the following databases to perform gene function annotation: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG.

[0029] Any method capable of analyzing gene expression and gene structure is applicable to the present application. In a preferred embodiment, the analysis module further includes: an expression analysis unit, which is configured to compare each gene in the genome to be quality assessed with a reference second-generation transcript using hisat2 software, and then convert the comparison result into the expression result of each gene using htseq software; preferably, the analysis module further includes: a gene structure analysis unit, which is configured to analyze whether there is a frameshift mutation in the gene in the genome, whether the number of bases in the CDS is an integer multiple of 3, and whether there is a correct start codon and a correct stop codon.

[0030] In order to quantify the above analysis results into an evaluation index that can be objectively evaluated, in a preferred embodiment, the judgment module includes: a scoring unit, which is configured to output a score of 100 points if the result of the gene to be evaluated by the BUSCO software is Completed or Duplicated, and a score of 50 points if it is Fragmented, otherwise no score; if the sum of the expression levels of the genes to be evaluated is greater than 1, the score is output as 100 points, otherwise no score; if the gene to be evaluated has functional annotation data in 3 or more databases, the score is output as 100 points, if the number of databases is 2, the score is output as 95 points, and if the number of databases is 1, the score is output as 90 points; if the gene to be evaluated has a frameshift mutation, no score is given, if there is no frameshift mutation, but there is no correct start codon and / or correct stop codon, the score output is plus 1 point, if there is no frameshift mutation and the start codon and the stop codon are correct, the score output is plus 2 points.

[0031] In order to accurately and observably associate the above-mentioned analysis results with the annotation quality of the genome, in a preferred embodiment, the output result unit is set to use the median of the scores of all genes to be quality assessed in the genome as the final score of the genome to be quality assessed, and use the final score to judge the annotation quality of the genome to be quality assessed; if the final score is ≥90 points, the annotation quality of the genome to be quality assessed is output as excellent; if the final score is ≥60 and <90 points, the annotation quality of the genome to be quality assessed is output as good; if the final score is <60 points, the annotation quality of the genome to be quality assessed is output as unqualified; wherein the score does not exceed 100 points.

[0032] In a third typical embodiment of the present application, a computer-readable storage medium is provided, the storage medium including a stored program, wherein when the program is executed, the device where the storage medium is located is controlled to execute the above-mentioned method for evaluating the annotation quality of a genome.

[0033] In a fourth typical embodiment of the present application, a processor is provided, and the processor is used to run a program, wherein the program runs the above-mentioned method for evaluating the annotation quality of a genome.

[0034] The present application is further described in detail below in conjunction with specific embodiments. These embodiments should not be construed as limiting the scope of protection claimed in the present application.

[0035] Embodiment 1

[0036] In this embodiment, the genome annotation quality detection is performed as follows: Subgenome.

[0037] 1. Use BUSCO software to select the embryophyta_odb10 library pair The subgenome (allotetraploid genome) was analyzed for single-copy orthologous gene integrity, and the Busco evaluation result full_table.tsv was obtained.

[0038] 2. Use the following database to The subgenomes were functionally annotated using SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG to obtain the functional annotation results of each gene;

[0039] 3. Use hisat2 software to The subgenome was compared with the reference second-generation transcripts, and the comparison results were converted into genome expression results using htseq software;

[0040] 4. Analysis The coding sequence structure of each gene in the subgenome is tested for frameshift mutations, non-triploidy, correct start codons, and correct stop codons;

[0041] 5. Use the above analysis results to evaluate Subgenomes are scored:

[0042] If the result of the gene to be evaluated by BUSCO software is Completed or Duplicated, the score is 100 points, if it is Fragmented, the score is 50 points; if the sum of the expression levels of the genes to be evaluated is greater than 1, the score is 100 points, otherwise no score; if the gene to be evaluated has functional annotation data in 3 or more databases, the score is 100 points, if the number of databases is 2, the score is 95 points, and if the number of databases is 1, the score is 90 points; if the gene to be evaluated has a frameshift mutation, no score is given; if there is no frameshift mutation but there is no correct start codon and / or correct stop codon, the score is increased by 1 point; if there is no frameshift mutation and the start codon and stop codon are correct, the score is increased by 2 points; among them, the score does not exceed 100 points.

[0043] If the score is ≥90, the annotation quality of the gene to be evaluated is excellent; if the score is ≥60 and <90, the annotation quality of the genome to be evaluated is good; if the score is <60, the annotation quality of the genome to be evaluated is unqualified. The score results for each gene in the sub-gene set are shown in Table 1 below:

[0044] Table 1:

[0045]

[0046] The four-digit number pair in the gene structure integrity in Table 1 above is an evaluation of the gene structure, 0 means there is a problem, and 1 means it is correct. The numbers from left to right represent whether the gene has the correct start codon, the correct stop codon, whether it is frameshifted (non-triplicated), and whether there is an internal stop codon (early termination).

[0047] The overall evaluation results obtained using the method of this application are:

[0048] The total number of genes in the subgenome is 66508, of which 64535 have excellent annotation quality, 0 have good annotation quality, and 1973 have unqualified annotation quality. Genes with unqualified annotation quality can be deleted according to actual needs. The overall score of the annotation evaluation of the subgenome is: 97.10, that is The annotation quality of the subgenomes is excellent.

[0049] 6. Existing technology: Using BUSCO software to The sub-genomes were evaluated, and the evaluation results are shown in Table 2:

[0050] Table 2:

[0051]

[0052] Using BUSCO software The score for evaluating the annotation quality of the subgenome is 98.2. Although the score is an excellent result, only the quality of 1614 direct single-copy genes was detected, and the annotation quality of all genes in the genome could not be evaluated. The results obtained may be inconsistent with the actual situation. It can be seen that the genome annotation quality assessment method of this application is more accurate.

[0053] From the above description, it can be seen that the above-mentioned embodiments of the present invention achieve the following technical effects: it is capable of performing multi-dimensional quality evaluation on each gene in the genome in four aspects: gene integrity, functional annotation, expression level and gene structure, and making a more accurate judgment on the annotation quality of the genome in a more comprehensive manner, which is of great significance to the reliability and applicability evaluation of genome data.

[0054] The above description is only a preferred embodiment of the present invention and is not intended to limit the present invention. For those skilled in the art, the present invention may have various modifications and variations. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present invention shall be included in the protection scope of the present invention.

Claims

1. A method for evaluating the annotation quality of a genome, characterized in that The method comprises: Perform single copy orthologous gene integrity analysis, gene function annotation, expression analysis and gene structure analysis on each gene in the genome to be assessed for quality, and obtain an analysis result file; Performing quantitative scoring on the analysis result file, and judging the annotation quality of the genome to be quality assessed based on the scoring result; The expression analysis of the genome to be evaluated for quality includes: Using hisat2 software, each gene in the genome to be evaluated for quality is compared with the reference second-generation transcript, and then using htseq software, the comparison results are converted into expression results of each gene; The gene structure analysis of the genome to be evaluated for quality includes: analyzing whether there is a frameshift mutation in the gene in the genome, whether the number of bases in the CDS is an integral multiple of 3, and whether there is a correct start codon and a correct stop codon.

2. The method according to claim 1, characterized in that Using BUSCO software or compleasm software to perform the single copy orthologous gene integrity analysis on the genome to be assessed for quality; The gene function annotation is performed using at least one of the following databases: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG.

3. The method according to claim 2, characterized in that The single copy orthologous gene integrity analysis was performed using the embryophyta_odb10 library in the BUSCO software.

4. The method according to claim 2, characterized in that: The criteria for quantitative scoring of the analysis result files are: If the result of the gene to be quality assessed is Completed or Duplicated by the BUSCO software, the score is 100 points; if it is Fragmented, the score is 50 points; otherwise, no score is given; If the sum of the expression levels of the genes to be evaluated is greater than 1, the score is 100 points, otherwise no score is given; If the gene to be quality assessed has functional annotation data in 3 or more of the databases, the score is 100 points; if the number of the databases is 2, the score is 95 points; if the number of the databases is 1, the score is 90 points; If the gene to be quality-assessed has the frameshift mutation, no score is given; if the frameshift mutation does not exist but there is no correct start codon and / or correct stop codon, 1 point is added to the score; if the frameshift mutation does not exist and both the start codon and the stop codon are correct, 2 points are added to the score; The average of the scores of all the genes to be quality assessed in the genome is used as the final score of the genome to be quality assessed, and the annotation quality of the genome to be quality assessed is judged based on the final score; If the final score is ≥90 points, the annotation quality of the genome to be quality evaluated is excellent; if the final score is ≥60 points and <90 points, the annotation quality of the genome to be quality evaluated is good; if the final score is <60 points, the annotation quality of the genome to be quality evaluated is unqualified; The score shall not exceed 100 points.

5. A device for evaluating the annotation quality of a genome, characterized in that The device comprises: An analysis module is configured to perform single copy orthologous gene integrity analysis, gene function annotation, expression analysis and gene structure analysis on each gene in the genome to be evaluated for quality, and obtain an analysis result file; A judgment module is configured to perform quantitative scoring on the analysis result file, and judge the annotation quality of the genome to be quality assessed based on the scoring result; The analysis module also includes: an expression analysis unit, which is configured to compare each gene in the genome to be quality assessed with a reference second-generation transcript using hisat2 software, and then convert the comparison result into an expression result of each gene using htseq software; The analysis module also includes: a gene structure analysis unit, which is configured to analyze whether there is a frameshift mutation in the gene in the genome, whether the number of bases in the CDS is an integer multiple of 3, and whether there is a correct start codon and a correct stop codon.

6. The device according to claim 5, characterized in that The analysis module comprises: A gene integrity analysis unit is configured to perform the single copy orthologous gene integrity analysis on the genome to be quality assessed using BUSCO software or compleasm software; The analysis module further comprises: a gene function annotation unit, which is configured to perform gene function annotation using at least one of the following databases: SwissProt, NT, NR, PFAM, eggNOG, GO or KEGG.

7. The device according to claim 6, characterized in that The gene integrity analysis unit also includes: being configured to perform the single copy orthologous gene integrity analysis using the embryophyta_odb10 library in the BUSCO software.

8. The device according to claim 6, characterized in that The judgment module includes: a scoring unit, which is configured to output a score of 100 if the result of the gene to be quality assessed is Completed or Duplicated by the BUSCO software, and a score of 50 if it is Fragmented, otherwise no score; If the sum of the expression levels of the genes to be quality assessed is greater than 1, the score output is 100 points, otherwise no score is output; If the gene to be quality assessed has functional annotation data in 3 or more databases, the score output is 100 points; if the number of databases is 2, the score output is 95 points; if the number of databases is 1, the score output is 90 points; If the gene to be quality-assessed has the frameshift mutation, no score is given; if the frameshift mutation does not exist but there is no correct start codon and / or correct stop codon, the score output is increased by 1 point; if the frameshift mutation does not exist and both the start codon and the stop codon are correct, the score output is increased by 2 points; The output result unit is configured to take the median of the scores of all the genes to be quality assessed in the genome as the final score of the genome to be quality assessed, and to judge the annotation quality of the genome to be quality assessed based on the final score; If the final score is ≥90 points, the annotation quality of the genome to be quality evaluated is output as excellent; if the final score is ≥60 points and <90 points, the annotation quality of the genome to be quality evaluated is output as good; if the final score is <60 points, the annotation quality of the genome to be quality evaluated is output as unqualified; The score shall not exceed 100 points.

9. A computer-readable storage medium, characterized in that: The storage medium includes a stored program, wherein when the program is executed, the device where the storage medium is located is controlled to execute the method for evaluating the annotation quality of a genome according to any one of claims 1 to 4.

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