design: 1 Raw Data Processing: This step filters reads with low sequencing quality values, retaining high-quality reads. The filtered data is referred to as Clean Data.  2 Sample Assembly: Genome assembly is performed to obtain sequence files that reflect the sample's genome.  3 Genome Composition Analysis: After assembly, the components of the sample's genome are analyzed, including the prediction of coding genes, non-coding RNAs, repetitive sequences, prophages, gene islands, CRISPR, and other predicted genetic components.  4 Functional Annotation: Coding gene sequences are annotated functionally using different databases, including commonly used databases such as KEGG and COG, as well as databases for pathogenic microorganisms.  5 Genome Comparative Analysis: This step compares the differences between the sample and the reference genome at both the genome and gene levels, including collinearity analysis, gene family construction, analysis of shared/specific genes, and the construction of species phylogenetic trees.  6 Genome Visualization Analysis: Combining the results of genome composition analysis and functional annotation, this step presents the basic research findings of the genome.