This lesson is still being designed and assembled (Pre-Alpha version)

Genome Assembly

Genomic analyses may often be dependent on a reference genome assembly for a focal species. Reference genomes can be used to detect variant sites within or between populations with greater confidence than similar de novo approaches. As such, a first step in many population genomics projects will be sequencing and assembling a reference genome for the species of interest if no such resources yet exist.

This one day workshop is designed to show you how to assemble a genome through hands-on analysis of Nanopore long reads and Illumina short reads, and highlight key considerations for the various steps in the workflow.

Prerequisites

All pre-requisites are taken care of if you are using this lesson at the Otago Bioinformatics Spring School 2022.

Schedule

Setup Download files required for the lesson
00:00 1. Introduction What is genome assembly?
00:10 2. Using the slurm scheduler How to submit jobs to an HPC scheduler
00:30 3. Exploring input data and genome characteristics How do the characteristics of short-read and long-read datasets differ?
What underlying characteristics of a genome may complicate genome assembly?
01:50 4. Draft genome assembly What considerations should be taken into account when selecting a genome assembler?
02:10 5. Assessing assembly quality How do we know whether a genome assembly is of sufficient quality to be biologically accurate?
03:00 6. Assembly polishing and post-processing How can we improve a draft assembly to make it more correct and accurate?
04:00 Finish

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