About this Event
Title
Lead trainer:
Ashley Dungan
Workshop Description:
This workshop will give you an introduction to the QIIME2 analysis platform using 16S rRNA gene amplicon data from marsupial-associated bacteria.
Topics covered will be:
- Importing, cleaning and quality control of the data
- Taxonomic Analysis
- Building a phylogenetic tree and
- Basic visualizations and statistics.
Learning objectives
At the end of this introductory workshop, you will be able to:
- Describe the structure of amplicon sequencing data, including the components of raw 16S rRNA gene output (FASTQ files, barcodes, and metadata), and explain how sequencing depth, quality scores, and primer choice influence downstream analyses.
- Implement a reproducible QIIME2 workflow, from raw sequence import through denoising (DADA2), feature table construction, and taxonomic assignment.
- Calculate and interpret ecological diversity metrics, including alpha and beta diversity; understand rarefaction; and visualise ordinations (e.g., PCoA) to infer patterns of community similarity and clustering.
- Integrate microbiome structure with biological context, formulating hypotheses about captivity-associated microbial shifts in wild versus captive fat-tailed dunnarts (Sminthopsis crassicaudata).
- Critically evaluate the strengths and limitations of 16S rRNA gene amplicon data, including issues of compositionality, relative abundance, and functional inference.
Target audience:
Researchers new to the analysis of bacterial communities using 16s rRNA gene (full-length or amplicon) sequencing who have some command line experience.
Eligibility:
This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes.
You must register for this event using an affiliated institutional email address or your registration may be cancelled.
Prerequisites and Requirements:
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 you can review our online training in unix, or enroll in one of the "Introduction to Linux and HPC" workshops 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.
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).
Access:
If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements:
We recommend following our Eventbrite page if you wish to be alerted when we release new workshops for registrations. If you require any further information, please contact Melbourne Bioinformatics at: [email protected]
Important Policy Update:
Starting 1 August 2025, participants who miss two or more workshops without proper notice (less than 48 hours or attending under 50%) within 12 months will be placed on a 6-month waitlist for full workshops. To avoid being marked as a no-show, cancellations must be made at least 24 hours in advance, with exceptions allowed for emergencies.Please read the full policy here: https://mbite.org/guides/policy/
Event Venue & Nearby Stays
21 Bedford St, 21 Bedford Street, North Melbourne, Australia
AUD 0.00
