Method for quickly acquiring comparison result data of target genome region

Abstract

The invention discloses a method for quickly acquiring comparison result data of a target genome region. The method comprises the following steps: acquiring a reference genome sequence file and coordinate information files of all genes by using a public genome database on the basis of sample original sequencing data, and constructing a reference genome index file and a chromosome index file; constructing a mapping relationship between the sequence line number of the sample original sequencing data and genome comparison coordinates, and quickly reconstructing sample original sequencing data of a target gene sequence by using the mapping relationship; and carrying out sequence comparison by utilizing the chromosome index file and the sample original sequencing data of the target gene sequence to obtain an original comparison data file of the target gene sequence, and carrying out sequencing and duplicate removal to obtain final comparison result data of a target genome region. The method has the characteristics of simplicity in deployment, convenience in operation, high efficiency, high throughput and wide application range. Compared with an original secondary data BAM file, the obtained result basically has no information loss.

Description

technical field [0001] The invention relates to the technical field of genome variation detection in bioinformatics and precision medicine, and in particular to a method for quickly obtaining target genome region comparison result data based on original sequencing data of samples. Background technique [0002] With the rapid development of precision medicine, high-throughput sequencing technology (Next-Generation Sequencing, NGS) has gradually become the preferred method of genetic testing. The NGS sequencing of samples also brings a large amount of sequencing data, which leads to higher and higher requirements for computing power and storage of computers. At present, people classify NGS data according to different types. Different levels of data also have different requirements for storage forms. The general classification is as follows: [0003] a. The original data of the sample, usually the file format is FASTQ, is the first-level data, which needs to be stored for a lo...

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Problems solved by technology

[0009] b. Reducing the BAM still needs to occupy a certain amount of storage resources, and with the increase of the sample size, there is still a limitation of insufficient storage resources, so people have to face another problem, that is, how to solve the storage problem of reducing the BAM of a large number of samples

[0010] c. This method is not universal, and different data analysts have a preference for gene regions with functional genes, which has a strong correlation with the knowledge background of the analysts, so it will cause the same original sample The secondary data BAM file, after being reduced by different analysts, will generate a completely different reduced BAM file

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