Automatic analysis method and system for sequencing data of whole genome of bacteria

Abstract

The invention provides an automatic analysis method for bacterial whole genome sequencing data, which comprises the following steps: acquiring bacterial genome sequencing data, and judging the type of the sequencing data; respectively carrying out corresponding preprocessing according to the type of the sequencing data; performing re-sequencing analysis and de novo sequencing analysis on the preprocessed sequencing data according to an analysis type selected by a user and preset tool software and software parameters; and realizing the identification and annotation of the whole genome of the bacteria. The scheme provides a user-friendly automated analysis method, for researchers and clinicians without professional bioinformatics knowledge, automated bioinformatics analysis steps including sequencing quality control, re-sequencing and de novo assembly, similar bacterial reference genome identification, bacterial genome annotation, and at the same time, researchers and clinicians without professional bioinformatics knowledge; meanwhile, customized bioinformatics analysis can be carried out according to short-read-length and long-read-length sequencing data generated by different platforms, and an accurate analysis result is obtained.

Description

technical field [0001] The disclosure belongs to the technical field of gene sequencing, and in particular relates to an automatic analysis method and system for bacterial whole genome sequencing data. Background technique [0002] The statements in this section merely provide background information related to the present disclosure and do not necessarily constitute prior art. [0003] The widespread use of bacterial genome information requires automated workflows for genome sequencing analysis. Research on bacterial genome analysis workflows has achieved some results. [0004] The inventors found that the existing workflow for the whole genome of bacteria usually focuses on the analysis of the second-generation bacterial sequencing data, which cannot satisfy the current rapid development of the third-generation and even some fourth-generation sequencing technologies, which are characterized by long reads. Analysis requirements for the generated sequencing data. And the a...

AI Technical Summary

Problems solved by technology

[0004] The inventors found that the existing workflow for the whole genome of bacteria usually focuses on the analysis of the second-generation bacterial sequencing data, which cannot satisfy the current rapid development of the third-generation and even some fourth-generation sequencing technologies, which are characterized by long reads. Analysis requirements for the generated sequencing data

And the aspects they involve are usually not comprehensive enough, only focusing on a single aspect of de novo sequencing or resequencing

[0005] While existing metagenomic workflows usually focus on metagenomic assembly bins, abundance calculations, etc., and provide good analysis at the metagenomic level (metagenomics usually focuses on the species diversity and functional potential of the entire microbial community in the environment ), but ignores the in-depth analysis of individual bacterial genomes after strain isolation and screening, such as the identification of individual bacterial genomes (accurate to the strain level) and corresponding annotations, which have important applications in the breeding and improvement of industrial microbial strains

[0006] In addition, existing workflows generally offer fewer choices of analysis tools for sequence preprocessing and assembly, which are less user-friendly

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