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:
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June 25, 2024
- Session Recording
- Prokaryotic Genome Assembly
- Introduction Powerpoint
- Setting up the computers
- Hands-On Exercises
- Downloading Illumina SRR files from NCBI
- Illumina Genome Assembly
- Downloading PacBio and/or nanopore reads
- Long reads assembly
- Polishing
- Assembly evaluation
- Some curation
-
June 26, 2024
- Session Recording
- Eukaryotic Genome Assembly
- Introduction to eukaryotic genome assembly
- Hands-On Exercises
- Assembling Yeast genome with nanopore reads
- Genomescope2
- Nanofilt and filtlong
- Fly Assembly
- Evaluation
- Assembling Yeast Genome with HiFi reads
- HiFiAsm assembly
- Assembly Evaluation
- Polishing
- Some scaffolding
- Assembling Yeast genome with nanopore reads
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June 27, 2024
- Session Recording
- Introduction to HiC:
Hands-On exercises using an Arabidopsis dataset:- Aligning
- Scaffolding with hiC reads
- Haplotype phasing
- Assembly validation and Visualization