Introduction to long-read genome assembly

Overview

Presenter – Deiter Bulach

New genome sequencing technologies are producing much longer reads. This workshop combines an introductory presentation on the theory of de novo genome assembly with hands-on practice. We will use a cut-down data set of bacterial FASTQ reads from PacBio (long read) sequencing. Using command-line tools, we will assemble the reads with the tool Canu and correct the assembly with short read Illumina data.

Please note: This is a short workshop so we won’t cover the following: eukaryote data, nanopore reads, or a comparison of different assembly tools.

Learning objectives

By the end of this training, participants will be able to use some command-line tools for long-read genome assembly and polishing, on simple bacterial data sets.

Prerequisites and requirements

This workshop requires a basic familiarity with genomics concepts and Unix as the workshop is conducted on the command line. The Introduction to Linux workshop running on March 19 is a sufficient prerequisite.

This is a hands-on workshop and attendees must bring their own laptops to the workshop with the following software preinstalled:

• access to Uniwireless/Eduroam
• web browser (Firefox or Chrome recommended).