The Climate Change Cluster is working highly interdisciplinary using cutting edge technologies in the fields of genomics, transcriptomics, proteomics and metabolomics to further our understand of microbial ecology and biotechnology. In recent years these new technologies have led to a vast increase in biological data and data types requiring new bioinformatics tools and approaches for data processing and analysis. The bioinformaticians at C3 are actively developing tools and workflows for data analysis, integration and visualisation and make these available to the wider science community.
BASTA is a bioinformatics tool to estimate the taxonomy of genes and genome sequences based on a “Last Common Ancestor” (LCA) algorithm. It enables researchers to identify the origin of genetic sequences based on their similarity to known genomes at the National Center for Biotechnology Information (NCBI). BASTA is used for a variety of applications across C3 and Australia, such as filtering of contamination from coral-symbiont data, taxonomic classification of environmental sequences in the Australia-wide Marine Microbes project as well as the identification of algal sequences in photobioreactor sequencing projects.
Find out more about Basta.
Panbiom is a simple script to estimate the so called “core microbiome” of a given group of samples, i.e., it identifies the microbial species (OTUs) that are shared among all samples or treatments of interest. It is assumed that microbial species in the core microbiome play key roles in nutrient cycles and ecology of their respective environment.
Panbiom is used in many microbial community projects at C3 including our recently published core-microbiome analysis of the coral symbiont symbiodinium (Lawsen et al. 2017).
Find out more about Panbiom.
Ampli-tools is a collection of scripts and helper tools to facilitate the analysis of microbial community structure from sequencing reads. It includes scripts for sequence file manipulation and extraction of sequences from files and is part of the general marker gene sequencing pipeline at C3.
Find out more about Ampli-Tools.