Whole genome sequencing represents the determination of the complete DNA sequence of an organism’s genome at a single time, which entails chromosomal DNA as well as DNA contained in mitochondria and chloroplasts. Whole genome sequencing provides a powerful tool for both de novo sequencing and re-sequencing. De novo sequencing refers to sequencing of a novel genome without reference sequence available. The coverage quality of de novo assembly depends on the size and continuity of the contigs. De novo sequencing generates the first genome map for a species, thus providing a valuable reference sequence for re-sequencing. Oxford Nanopore and PacBio sequencing systems enable a faster and more accurate characterization of any species at the nucleotide level.