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  • Introduction
  • Webinar Agenda
  • Today's Presenters
  • Schatz: Assembly of Complex Genomes Using Single Molecule Sequencing
  • Assembly Complexity
  • PacBio Assembly Algorithms
  • Titration Experiment
  • Standard vs Spanning Coverage
  • Spanning Coverage Example
  • Consensus Accuracy and Coverage
  • What Should We Expect From an Assembly?
  • Acknowledgements
  • Gurtowski: Hybrid Error Correction with ECTools
  • Motivation for ECTools
  • Unitigs Are Longer Than Reads
  • Correction with Unitigs
  • How Can We Align Unitigs
  • MUMmer/Nucmer
  • Delta-Filter
  • Pipeline Workflow
  • ECTools Pipeline Walkthrough
  • Starting the Final Assembly
  • Important ECTools Parameters
  • E.Coli
  • Yeast W303
  • Arabidopsis
  • Assembly Results
  • Quality Control/Suggestions
  • Summary
  • Koren: Efficient Chromosome-Scale Assembly of Eukaryotic Genomes
  • Acknowledgement
  • Affordable Finished Genomes
  • Read Length Matters
  • Three Classes of Complexity
  • Longer Genome = Longer Contigs
  • Longer Repeats
  • Longer Runtime
  • MHAP: MinHash Alignment Process
  • MHAP Overlapping
  • MHAP Runtime
  • Code Demo: Phage Genome Assembly
  • Q&A Intro
  • QUESTION 1: What is the impact of polymorphisms on the quality of the assembly?
  • QUESTION 2: How do you assemble a genome bigger than 150 megabases only using PacBio reads with about 50x coverage?
  • QUESTION 3: CPU/memory data requirements?
  • QUESTION 4: Can other types of unitigs be used as inputs for ECTools?
  • QUESTION 5: Is it possible to mix the different sequencing chemistries while running programs like HGAP, CA, ECTools?
  • QUESTION 6: The consensus accuracy quoted for the results was taken before Quiver, right?
  • QUESTION 7: How can PacBio reads span 300 kb when they are actually shorter than 300 kb?
  • QUESTION 8: Are there any new wet lab developments that enable the isolation of longer fragments?
  • QUESTION 9: Have these algorithms been tested on polyploids or moderately heterozygous diploid genomes?
  • QUESTION 10: Should ECTools be used with only 5x biocoverage?
  • QUESTION 11: Is MHAP available as a standalone overlapper like BLASR?
  • QUESTION 12: Will the pipeline work for 350 megabase butterfly genome with 100x PacBio biocoverage, and which flag is used to activate Jason Chin's algorithm and is it the same as the Falcon assembler?
  • QUESTION 13: How does the run time of ECTools compare to PacBio?
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  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center
  • Speaker: Michael Schatz, PhD / James Gurtowski / Sergey Koren , PhD / Cold Spring Harbor Laboratory and National Biodefense Analysis and Countermeasures Center