Regular workshops

This is a list of all current workshops we have ready to go. If you are interested in any of these and they are currently not advertised, register your interest with our training team at bioinformatics-training@nullunimelb.edu.au.

Title  Brief description  Teaching interface  Typical duration 
Introduction to Genome Browsers  This hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrated Genome Viewer) using RNAseq gene expression data. Tools and public datasets will be used to illustrate how the expression of transcript variants can be investigated in different tissues and cell types using public data, including human RNAseq data from GTEX and mouse cell type RNAseq data from Tabula Muris, as viewed within the UCSC genome browser. A subset of aligned reads from the single cell RNAseq data Celltax study from the Allen Brain Atlas will also be downloaded from the SRA database and visualised in IGV. 

 

The training material used in this workshop is freely available here. 

Web based platform (UCSC genome browser) and locally installed software (IGV) on workshop participants own computer  4 hours 
QIIME2 analysis of bacterial 16s rRNA 

 

This workshop will give you an introduction to the QIIME2 analysis platform using 16S rRNA amplicon data from coral-associated bacteria. Topics covered include: importing, cleaning and quality control of the data, taxonomic analysis, building a phylogenetic tree, basic visualizations and statistics. 

 

The training material used in this workshop is freely available here. 

Command line interface using remote (Cloud) computer  4 hours 
Variant calling using GATK4 command line workflow  This workshop aims to introduce participants to variant calling using command line applications. The material follows the GATK variant calling best practices workflow and provides an introduction to tools, datatypes and file formats associated with variant calling. The workshop will use a test llumina sequencing dataset to progress through the workflow from aligning sequencing reads to a reference genome before applying the GATK best practices workflow to call genetic variants (SNVs and Indels) in test data. 

 

The training material used in this workshop is freely available here. 

Command line interface using remote (Cloud) computer  4 hours 
Introduction to Galaxy  This beginners tutorial will introduce Galaxy’s interface, tool use, histories. Click on these links to learn about Galaxy and available training material 

Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web. 

The material covered in this workshop is freely available at this link. 

Web based platform (Galaxy)  3 hours 
RNA-seq analysis: from reads to differentially expressed genes. 

 

Across 2 days (3 hours each day) attendees can expect to gain an understanding of approaches to and practical experience in: quality control of short reads, alignment, gene counts, data normalisation, differential expression and visualisation. Discussion is encouraged and experienced RNA-seq and Galaxy trainers will be present to answer your questions. 

The workshop materials are based on the following Galaxy training workshops which are freely available at the links below: 

Web based platform (Galaxy)  6 hours across 2 days. 
Hybrid de novo genome assembly – Nanopore and Illumina  Performing de novo assembly is easier than ever thanks to advances in long read sequencing and platforms such as Galaxy which enable bioinformatics workflows for non-coders. In this tutorial we will use the web-based analysis platform “Galaxy” to create a high-quality assembly of a Bacillus Subtilis strain. The software tools “Flye” and then “Pilon” will be used to perform the assembly and subsequent error correction to improve the accuracy of assembled contigs. You will learn how to will visualize input read sets and the assemblies produced at each stage and assess the quality of the final assembly.  

The training material used in this workshop is freely available here. 

 

Web based platform (Galaxy)  3 hours 
Structural Variant Calling using Long Read Data  In this training workshop you will gain an introduction to structural variation calling using long read data.  We will discuss what structural variants are, their importance in medicine and biotechnology, and how they are identified and visualised using modern online bioinformatics tools. We will also touch on the interpretation of our SV calls, by calculating performance metrics for our SV caller, sniffles. 

There is currently no ‘best practise’ for SV calling. The bioinformatics analysis will include a discussion of the initial data and use a workflow consisting of read alignment with minimap2, SV calling with sniffles, text reformatting of VCF files with awk, and visualisation with circos to perform our analysis.  

Benchmarking will be performed on our SV caller – sniffles – to estimate its accuracy, precision and recall. This performance information will be vital as we switch to a human read set, as will permit better interpretation of the results.  

The training material used in this workshop is freely available here. 

Web based platform (Galaxy)  4 hours 
Introduction to R for Biologists  This introduction to R and RStudio will provide beginners with experience with loading, manipulating and visualising biological data using the tidyverse collection of R packages. The example data used is publicly available RNA-seq data, therefore attendees will gain experience in the structure and appearance of RNA-seq data. 

At the end of the course, you will be able to: 

•    Load tabular data into R 

•    Apply tidyverse functions to manipulate data in R 

•    Produce simple plots such boxplots using ggplot 

•    Understand and apply data faceting in ggplot 

•    Modify the aesthetics of a ggplot plot. 

The training material used in this workshop is freely available here. 

Locally installed software (Rstudio) on workshop participants own computer, or web based platform (Rstudio cloud)  3 hours