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  • Introduction
  • Hierarchical Genome Assembly Process
  • Progress of PacBio Only De Novo Assembly
  • Sequencing Plan for Generating a "Synthetic" Diploid Dataset
  • String Graph
  • An Example
  • "Untangle" the Knots!
  • Apply the Best Overlapping Rule on the E. coli String Graph
  • Simplify the String Graph
  • Challenge of Diploid Assembly
  • Variations (or Errors) Induce Simple Bubbles
  • Example for the Input Data: Length Distribution of the Preassembled Reads For Assembly
  • Resolve Repeats By Long Read Lengths
  • Diploid: Different Large - and Small-Scale Topological Features
  • The Plan
  • From a "String Bundle" to a Primary Contig + Associated Contigs
  • Distinguish Vertices in the Bundle from Those in Branching Paths
  • Result I: Haploid Assembly of Col-0 (inbred line)
  • Result II: Haploid Assembly Ler-0 (inbred line)
  • Result III: "Diploid Assembly": Ler-0 + Col-0
  • Identify Structure Variations between Homologous Copies
  • Next: Unzipping the Bubble with SV + SNP Phasing
  • Acknowledgments, Data Sets & Code
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  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio
  • Speaker: Jason Chin, PhD / PacBio