Hybrid de novo genome assembly – Nanopore & Illumina – online

Overview

Presenter – Grace Hall Most modern bioinformatic analyses are not possible without high-quality reference genomes. They are the backbone that supports current and future discoveries, and our collection of complete genome sequences are one of humanity’s greatest achievements. Performing de novo assembly is easier than ever thanks to advances in long read sequencing and platforms such as Galaxy which enable bioinformatics workflows for non-coders. In this tutorial we will use the web-based analysis platform “Galaxy” to create a high-quality assembly of a Bacillus Subtilis strain. The software tools “Flye” and then “Pilon” will be used to perform the assembly and subsequent error correction to improve the accuracy of assembled contigs. You will learn how to will visualize input read sets and the assemblies produced at each stage and assess the quality of the final assembly.

Tools used

Galaxy, Flye, Pilon

Learning objectives

By the end of this training, participants will:

• understand how Nanopore and Illumina reads can be used together to produce a high quality genome assembly
• be familiar with genome assembly and polishing programs
• be able to perform de novo assembly using Nanopore and Illumina reads!

Prerequisites and Requirements

This workshop does not require any previous experience with working with sequencing reads, but familiarity with Galaxy and Galaxy workflows, or completion of “Introduction to Galaxy” workshop is required. This is a hands-on workshop and attendees must bring their own laptops to the online workshop with the following software preinstalled:

• access to internet
• web browser (Firefox or Chrome recommended)
• Zoom (Version 5.1 or higher)

Our workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes (registering with their institutional email). Due to high demand locally, for the remainder of 2020, we will not be taking any external paying applicants. For further details, please see the Melbourne Bioinformatics Training page.