We are proposing a pipeline including de novo genome assemblywhole genome SNP array design to improve the practice in precision medicineprecision agriculture. We design GABOLA, a de novo genome assembly system, combining advantages in leading sequencing platform, to construct completeaccurate individual genomes. GABOLA can resolve large structural variants, fills the gap in human reference genome,avoid the bias from reference genome. We combine the knowledge of population geneticsfunctional information to design whole genome SNP array to aid future genomic study.

To assess the performancevalue of GABOLA, we set Supernova, the genome assembler designed by 10X Genomic, as benchmark to evaluate the improvement we gain on GABOLA. GABOLA significantly improves genome assembly on genome completeness, scaffold contiguityinterpretation on genetic functionality. The improvement enables researchers to explore gap regionsgather knowledge on large structural variationsfunctionally important genes. The design of SNP array can improve trait selection process on the genome-wide scalecan be applied to diverse traits of interests.

Establishment of completeaccurate individual genome is the cornerstone of precision medicinewill become future standard practice in precision agriculture. Researchers can first collect samples to perform whole genome sequencing,assembly the genome by GABOLA. This improve the interpretations on personal diseases. SNP array covering pervasive SNPs in the genometraits-related variants that are of user＇s interests can be designed. The practitioners in the field can easily apply the SNP array to gather useful genetic informationpromote the improvement in field practices.

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