Introduction to metagenomic profiling with nf-core

Claudio Díaz García, Trang Nguyen (Melbourne Bioinformatics, The University of Melbourne)

Wednesday 4th November 10am-2pm

Thursday 5th November 10am-2pm

This workshop will give you an introduction to taxonomic and functional classification and profiling of human gut microbiome using metagenomic data

Topics covered will be:

1. Using workflow manager
2. Shotgun metagenomics analysis using nf-core pipeline
3. Taxonomic profiling and analysis
4. Interpreting outputs from different taxonomic profilers, using different reference databases
5. Functional profiling and analysis
6. Basic visualisations and statistics.

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

Day 1:

• Understand the concept of the metagenomic approach and its added values over amplicon sequencing in studying human gut microbiome
• Gain hands-on experience with a workflow manager (Nextflow) and its importance in maintaining research reproducibility
• Set up, prepare inputs, and run nf-core/taxprofiler, bioinformatics best-practice analysis pipeline for for taxonomic classification and profiling of WGS metagenomic data
• Set up, prepare inputs, and run nf-core/funcprofiler, bioinformatics best-practice analysis pipeline for for functional classification and profiling of WGS metagenomic data
• Understand and interpret concepts such as relative abundance, gene-family abundance, pathway abundance and coverage

Day 2:

• Understand the fundamental difference between relative sequence abundance and relative taxonomic abundance, and how each type influence the biological interpretation
• Evaluate the pros and cons of different taxonomic/functional profilers and databases
• Familiarise with R-native data types frequently used in microbiome statistical analysis (e.g., TreeSummarizedExperiment)
• Calculate and interpret ecological diversity metrics from taxonomy table, including alpha and beta diversity; understand rarefaction; and visualise ordinations (e.g., PCoA) to infer patterns of community similarity and clustering.
• Define an appropriate differential-abundance question and conduct statistical test to answer the question
• Understand the biological complexity of the microbial community and critically choose an appropriate methodology for the research question(s)

Researchers new to the analysis of bacterial communities using metagenomics who have some experience with command-line interfaces, R, and RStudio.

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.

This workshop requires previous experience with R and the command line. This is an in-person, hands-on workshop and attendees must bring their own computers (laptop chargers also recommended). The following is required:

• Access to internet via uniwireless or Eduroam
• Web browser (Firefox or Chrome recommended)
• R and RStudio installed
• Use of the terminal (Mac/Linux) or PuTTY installed (Windows)

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]

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.mdhs.unimelb.edu.au/guides/policy/