Method for judging saturation of sequencing data, computer readable medium and application

Abstract

The invention provides a method for judging the saturation of sequencing data, a computer readable medium and an application, and relates to the field of sequencing technology. The method comprises the steps of: (a) providing the sequencing data, the sequencing data being a data set A comprising X reads; (b) clustering the X reads according to a preset sequence similarity threshold to generate N Clusters; (c) obtaining Probalility; the Probalility being the probability that the number of Clusters obtained by extracting the k-1-th read is i-1, one reads is then extracted, and the number of Clusters obtained is i; wherein k is a positive integer less than or equal to X, and i is a positive integer less than or equal to N; and (d) obtaining an index Saturated that measures the degree of saturation of the data, the more the data saturation degree index Saturated approaches zero, the more the sequencing data tend to be saturated. The method can accurately reflect the saturation degree of the sequencing data by numerical value, so that the saturation of the sequencing data can be judged more accurately, so as to ensure the accuracy of subsequent data analysis.

Description

technical field [0001] The present invention relates to the technical field of sequencing, in particular to a method for judging the saturation of sequencing data, a computer-readable medium and an application. Background technique [0002] Sequencing technology refers to the analysis of the base sequence of nucleic acid. For example, DNA sequencing is to analyze the arrangement of adenine (A), thymine (T), cytosine (C) and guanine (G) in DNA. Since the dideoxy chain termination sequencing technology established by Fredrick Sanger et al. in 1977, sequencing technology has undergone rapid development for decades. Since 2005, the emergence of next-generation sequencing technologies represented by Roche454, Illumina, Life SOLID / Ion Torrent, and PacBio RS has rapidly increased the throughput of sequencing and greatly reduced the cost of sequencing. [0003] High-throughput sequencing (High-throughput sequencing) technology can simultaneously sequence millions of DNA molecules, ...

AI Technical Summary

Problems solved by technology

[0006] The main indicator to measure the amount of sequencing data is the sequencing depth. The sequencing depth refers to the ratio of the total number of bases obtained by sequencing to the size of the genome to be tested. It can be understood as the average number of times each base in the genome is sequenced. Sequencing depth = reads Length × number of aligned reads / length of the reference sequence. Since the amount of data read from each fragment on the target fragment is not uniform during sequencing, the sequencing depth cannot clearly reflect whether the sequencing data is saturated or whether there are undetected fragments.

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