Workshop: Microbial Genome Assembly using Short Sequencing Reads
On 13 and 14 May, NeSI and Genomics Aotearoa will be hosting an online workshop on Microbial Genome Assembly using Short Sequencing Reads. The workshop will be taught from 9:00am–1:00pm NZT on both days and we welcome interest from New Zealand researchers interested in learning how to assemble microbial genomes using short-read sequencing data.
This workshop will cover:
- The principles of microbial genome assembly using short sequencing reads.
- Differences between de novo and reference-guided assembly approaches.
- Hands-on walkthrough of a genome assembly workflow.
- Key considerations such as sequencing read length, depth, and contamination.
- Genome annotation and visualisation techniques.
- Practical examples using Microcoleus cyanobacterial sequencing data.
Please confirm you meet the following prerequisites for this advanced workshop.
Prerequisites
This workshop assumes some familiarity with the command line and basic R. You should be comfortable with:
- Navigating files and directories in a shell environment.
- Slurm and HPC environments.
- Using command-line tools to manage files.
- Basic R for visualisation (e.g., reading and exploring data).
If you are unfamiliar with these skills, we recommend completing an Introduction to Shell or R workshop with us (or an equivalent) before attending.
Setup
This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.
Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.
In case of any questions, please reach out to training@nesi.org.nz
