Software

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.

DIGS

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

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.

Diversi Tools

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

GLUE is a protocol for working with mutiple sequence alignments (MSAs) and for generating standardized reports using MSAs and data. GLUE also provides tools for managing MSAs and data, and can be used in combination with the MySQL relational database management system (RDBMS) to create boutique sequence databases

HCV GLUE

The HCV online web service is a HCV sequence database and supports analysis of hepatitis C virus (HCV) sequence data using the GLUE framework.

Tanoti

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

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.

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