Method and device for identifying microbial contamination in second-generation targeted capture sequencing sample

Abstract

The invention relates to the technical field of gene sequencing and bioinformatics, and provides a method for identifying microbial contamination in a second-generation targeted capture sequencing sample, a corresponding device for executing the method and a computer readable storage medium. The method comprises a targeted capture sequencing original data processing step, a human reference genomecomparison step and a serious microbial contamination judgment step, and further comprises a contaminated microorganism variety and content identification step in a sample. The method provided by theinvention can qualitatively identify whether serious microbial contamination exists in the sequencing sample or not, can further quantitatively identify the variety and content of contaminated microorganisms, and has important application prospects in sequencing and analysis of clinical samples.

Description

technical field [0001] The invention relates to the technical fields of gene sequencing and bioinformatics, in particular to a method and device for identifying microbial contamination in a second-generation targeted capture sequencing sample. Background technique [0002] Next-generation DNA sequencing (NGS) is a massively parallel sequencing technology that can simultaneously sequence hundreds of thousands to millions of DNA molecules contained in a sample at a time, so it is sensitive and efficient. Targeted capture sequencing is to first capture the specific DNA sequence contained in the sample, and then sequence the captured sequence. Currently, targeted capture sequencing technology is mainly used in the detection of human clinical nucleic acid samples, but these clinical samples often contain different degrees of microbial contamination. Microorganisms may come from human pathogenic microorganisms, intestinal flora microorganisms, and environmental microorganisms. Th...

AI Technical Summary

Problems solved by technology

Currently, targeted capture sequencing technology is mainly used in the detection of human clinical nucleic acid samples, but these clinical samples often contain different degrees of microbial contamination

Microorganisms may come from human pathogenic microorganisms, intestinal flora microorganisms, and environmental microorganisms. These microbial contaminations will bring microbial sequence information to sequencing samples, affect the quality of human clinical nucleic acid sequencing libraries, and even lead to the failure of human clinical sample sequencing

There is no microbial contamination identification step in conventional next-generation targeted capture sequencing workflows

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