This course provides a systematic overview of core computational modules in genomics research. The first chapter introduces genome survey analysis, explaining how K‑mer‑based methods estimate genome size, heterozygosity, and repeat content using tools such as GenomeScope to guide sequencing strategy design. The second chapter focuses on de novo genome assembly, comparing Sanger, NGS, and third‑generation sequencing technologies, and explaining assembly principles (read merging and scaffold construction), popular software (Hifiasm, Verkko, etc.), and key quality metrics (N50, coverage, error rate). Multi‑dimensional evaluation frameworks are emphasized, including Merqury (K‑mer‑based accuracy), BUSCO (gene‑space completeness), and LAI (LTR retrotransposon integrity). The third chapter covers genome annotation: repeat classification and EDTA pipelines, protein‑coding gene prediction integrating homology‑based, transcriptome‑based, and ab initio approaches via MAKER/EVM integration, non‑coding RNA detection (tRNA, rRNA, miRNA), and functional annotation using NR, KEGG, GO, and KOG databases. The fourth chapter addresses Hi‑C 3D genomics, from 3C/4C/5C to Hi‑C, and explains hierarchical chromatin structures including chromosome territories, A/B compartments, TADs, and loops, along with Hi‑C‑assisted chromosome‑level assembly and applications in structural variation and gene regulation studies. The course integrates theory with practice, providing robust guidance for high‑quality genome research.