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Genome Assembly Workshop



In this interactive, hands-on workshop, you will learn how to use SCINet’s computing resources to convert raw DNA sequencing data into a complete genome assembly. Along the way, you will also learn best practices for ensuring that your genome assemblies are robust and useful for downstream analyses. Anyone with at least a little command-line experience (you don’t need to be an expert!) is welcome to join us!

In this workshop, we will cover the following topics:

  • Assembly Fundamentals: Understand the assumptions and limitations in genome assembly due to biology, sequencing technology, and assembly tools.
  • Hands-On Coding: Complete a genome assembly from start to finish: quality control, assembly, scaffolding, and polishing.
  • Evaluation of Assemblies: Not all genomes are equal! Gain the expertise to critically assess the quality of a genome assembly.

To register, please fill out this form

Remote

Schedule:

  • June 25, 2024

    • Session Recording
    • Prokaryotic Genome Assembly
      1. Introduction Powerpoint
      2. Setting up the computers
    • Hands-On Exercises
      1. Downloading Illumina SRR files from NCBI
      2. Illumina Genome Assembly
      3. Downloading PacBio and/or nanopore reads
      4. Long reads assembly
      5. Polishing
      6. Assembly evaluation
      7. Some curation

  • June 26, 2024

    • Session Recording
    • Eukaryotic Genome Assembly
      1. Introduction to eukaryotic genome assembly
    • Hands-On Exercises
      • Assembling Yeast genome with nanopore reads
        1. Genomescope2
        2. Nanofilt and filtlong
        3. Fly Assembly
        4. Evaluation
      • Assembling Yeast Genome with HiFi reads
        1. HiFiAsm assembly
        2. Assembly Evaluation
        3. Polishing
        4. Some scaffolding

  • June 27, 2024

    • Session Recording
    • Introduction to HiC:
      Hands-On exercises using an Arabidopsis dataset:
      1. Aligning
      2. Scaffolding with hiC reads
      3. Haplotype phasing
      4. Assembly validation and Visualization