The goal of the viral genomics and bioinformatics team is to lead the development of novel sequencing and analytical approaches focused on studying viruses and virus-host interactions. Below you will find summaries and links to a number of bioinformatic tools that have been developed within the CVR.
The database-integrated genome-screening (DIGS) tool provides a framework for implementing automated in silico screening of sequence databases using BLAST in combination with a relational database (MySQL).
DisCVR is a Diagnostic tool for detecting known human viruses in clinical samples from Next-Generation Sequencing (NGS) data. The tool uses a simple and straightforward Graphical User Interface and is optimized on Windows OS without compromising speed and accuracy.
DiversiTools is a computational tool that is specifically tailored towards viral HTS data sets and the analysis of the underlying viral populations that they represent. It was initially developed in collaboration with a number of virologists interested in characterising the intra-host diversity of viral populations and studying their evolution across transmission chains at the micro-evolutionary scale.
GLUE is a flexible data-centric bioinformatics environment for virus sequence data, with a focus on virus evolution and genomic variation. GLUE has been applied to a range of viruses. A GLUE-based resource focused on Hepatitis C virus is HCV-GLUE.
Tanoti is a BLAST guided reference based short read aligner. It is developed for maximising alignment in highly variable next generation sequence data sets (Illumina).
ViCTree is a bioinformatic framework that automatically selects new candidate virus sequences from GenBank, generates multiple sequence alignments, calculates a maximum likelihood phylogeny and integrates the sequences into the existing phylogenetic trees. For more information click here.