Long-read de novo assemblies: Raw data, assemblies and comparisons

Genetwister Technologies B.V. and Applied Bioinformatics, Wageningen University & Research are pleased to invite you to Long Read Sequencing Genomics Workshop.

General Information

In this two day workshop you will learn about two most common long read sequencing technologies: Pacific Bioscience an Oxford Nanopore Technology. You will learn how to work with the data, perform assembly, mapping, and compare the results of both technologies.

Who: The workshop is intended for bioinformaticians or researchers who want to learn about application of latest sequencing technologies in genomics. No prior experience with PacBio or ONT sequencing data is required.

Prerequisites

This two-day workshop is aimed at providing a basic understanding of creating and evaluating de novo assembly using long read technologies. The workshop requires knowledge of working with the Linux operating system and of biological topics such as genetics and DNA. The target audience consists of Master/PhD students or researchers working in the Life Sciences. Although the data is from a plant genome, the learned principles can be applied to many other organisms, including bacteria, fungi and mammals. The idea behind this workshop is that you learn the most by doing and discussing the results.

Schedule

Setup Download files required for the lesson
00:00 1. Introduction Introduction into long read sequencing
What is a de novo assembly?
00:20 2. Setup for the workshop Installation of the VirtualBox image
00:40 3. QC and evaluation of long read data How to determine basic statistics on read sets
What do these statistics mean: are they good or bad?
What are read technology specific errors?
02:10 4. Assembly of long reads (and Illumina reads) How do you assembly NGS reads to create a de novo assembly?
What type of information is given by the assembler?
04:40 5. Comparison and visualization of long read assemblies How do you compare draft assemblies with mummerplots?
How do you visualize repeat content?
07:10 6. Validation of assemblies What is the quality of my assembly on a nucleotide level?
What impact does a SNP have on gene structure and function?
09:40 7. Summary of obtained results and closing What is the best assembly?
How did you come to that conclusion?
09:50 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.