A11
1 Raw data processing This step filters out reads with low sequencing quality values, retains high-quality reads, and the filtered data is called Clean Data;2 Sample assembly Genome assembly is performed to obtain sequence files that reflect the genome of the sample;3 Genome composition analysis After assembly is complete, the composition of the sample genome is analyzed, including the prediction of components such as coding genes, non-coding RNAs, repetitive sequences, prophages, gene islands, CRISPR, and other genetic components;4 Functional annotation Functional annotation is performed on the coding gene sequences 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 samples and reference genomes at both genome and gene levels, including collinearity analysis, gene family construction, analysis of shared/specific genes, and species phylogenetic tree construction;6 Genome Visualization Analysis Combines the results of genome component analysis and functional annotation to present the basic research findings of the genome.