Vista

Virulence and genotype annotation tool for Vibio cholerae

Review of the distribution of biotypes and serotypes have identified issues with the initial selection of reference genes used by Vista. We are in the process of reviewing process and hope to have a resolution soon.

For now, please do not use the biotype and serotype assignments. The cgMLST clustering and core SNP tree methods provide a more robust and higher resolution view in any case.

About

The Vista tool provides biotype, and serogroup assignments, along with identification of virulence markers and functionally associated clusters of virulence genes.

Method

Submitted genomes are searched against a library of representative genes using blastn along with curated E-value and percent identity thresholds. These matches are then used to infer the genotypes and presence of known virulence factors in V. cholerae.

The FOSS licensed software and databases can be found on Github.

Results

Genotypes

The biotype and serogroup are shown individually in the "Genotyping" section of the Genome Report and Collection View "Typing" table.

Virulence

In the genome report, the virulence genes and clusters are split into two sections: "Virulence genes", which contains individual determinants of virulence, and "Virulence clusters", which contains sets of interacting virulence genes. Generally all genes would be required to be present for the virulence phenotype to be expressed. The function of each cluster or gene is also shown in the virulence tables.

In the Collection View, virulence markers are shown in the "Virulence" table. One column is present for each individual determinant, while a single column is shown for each cluster. Red indicates the presence of the factor, while yellow indicates some of the members of a cluster are present.

Credits

This tool was developed by Corin Yeats, Sina Beier and Avril Coghlan.

How to cite

Manuscript in preparation

The software is available under an OSS licence from https://github.com/pathogenwatch-oss/vista