Recent advances in whole genome sequencing have significantly driven down the associated costs of sequencing and increased the throughput and availability of genetic information to the biomedical research field. However, major roadblocks to discovery and innovation still stand in spite of these breakthroughs. Namely, the read length of Next-Generation Sequencing technologies is relatively short. With the relatively short read length, whole genome resequencing studies are quite good at identifying single nucleotide variants (SNVs), but are notoriously unreliable at identifying small indels, larger insertions and deletions, and structural variants, and it is not possible to phase the variants using short reads without considerable additional experimentation. Specifically, we will develop technology that will ultimately allow us to sequence and assemble whole genomes, and identify all genetic variants and phase the genetic variants across entire chromosomes. We will accomplish our goals by scaffolding short reads along long DNA molecules, and scaffolding the short reads will solve key problems in genomics and allow for high quality de novo genome.