QIIME2 analysis of bacterial 16s rRNA

Workshop date: Thursday 6th October 2022

EOI deadline: 5pm Friday 23rd September 2022

Successful applicants notified: Wednesday 28th September 2022

Lead trainers:

Ashley Dungan (School of Biosciences, The University of Melbourne) Kshitij Tandon (School of Biosciences, The University of Melbourne)

Target audience:

Researchers new to analysis of bacterial communities using16sRNA who have some command line experience. Due to the limited number of places available at this workshop, places will be allocated based on this expression of interest application. Please complete the registration questions and submit them before the deadline. Successful applicants will be contacted one week prior to the workshop.

Eligibility:

This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section).

Required prerequisites:

Knowledge/experience of the command line is necessary for this workshop. You will need to be able to “ssh” into a remote machine, navigate the directory structure and “scp” files from a remote computer to your local computer. If you wish to attend a refresher course we recommend you attend the “Command line skills in UNIX” workshop on Oct 4th, or enroll in the “Introduction to Linux and HPC workshop” delivered regularly by Research Computing Services. This is a hands-on workshop and attendees must supply their own charged laptop with access to the internet/wifi and the following software preinstalled:

• Windows users: A terminal emulator such as PuTTY (free and open-source) will need to be downloaded.

• Software for file transfers between a local computer and remote server such as WinSCP or FileZilla.

• Mac users: No additional software needs to be installed for this workshop.

Workshop description:

This workshop will give you an introduction to the QIIME2 analysis platform using 16S rRNA amplicon data from coral-associated bacteria. The training material covered in this workshop is freely available here.

Topics covered will be:

1. Importing, cleaning and quality control of the data
2. Taxonomic Analysis
3. Building a phylogenetic tree and
4. Basic visualizations and statistics.

At the end of this introductory workshop, you will be able to:

• Take raw data from a sequencing facility and end with publication quality graphics and statistics
• Answer the question “What is the influence of genotype (intrinsic) and environment (extrinsic) on anemone-associated bacterial communities?”

This workshop is designed for participants with command-line knowledge. It will be run on a Nectar Instance. You will be given an individual IP address and password to log on to using the SSH client tool on your computer (Terminal on Mac or PuTTY on Windows). If you require any further information, please contact Melbourne Bioinformatics at: bioinformatics-training@nullunimelb.edu.au