To enable biologists to fully explore and integrate data, the omics.data.edu.au website provides a suite of tools for analysis, processing, and visualisation of multi-omic information. These tools will be available through the microbial Genomics Virtual Laboratory (mGVL). The mGVL includes a range of applications such as Galaxy, RStudio, Jupyter Notebook and even provides a Lubuntu desktop in the browser with access to command line tools.
To support Phase I, the Bioplatforms Australia’s Antibiotic Resistant Pathogens Initiative, there is a focus on tools for supporting microbial data analysis. For example, tools now available in mGVL’s Galaxy simplify the task of microbial genome assembly (Spades), annotation of genomic features (Prokka), identification of variants such as possible mutations (Snippy) and determine whether some genes are more highly expressed in particular conditions (Voom/Limma). Through the mGVL dashboard, an exciting new capability is to install the analysis platform SMRT portal for assembling long sequence reads from the PacBio machines.
Tutorials and workflows are being developed on the basis of these tools, and the list of included tools will grow with demand for the microbial omics data platform.