Vista

About

A database and genome assembly search tool for identifying Vibrio cholerae biotypes and serotypes, and identifying virulence genes and clusters.

This tool is currently under development by the CGPS. Please open an issue or contact us via email if you would link to know more or contribute.

How to use

Vista takes a DNA sequence FASTA file as input and outputs a JSON format result to STDOUT. While it will run directly on the command line, we only support building and running Docker images. To create a local or bespoke build, we recommend building a Docker image using the provided Dockerfile. However, it is straightforward to install and run locally using Python3 + BLAST.

Running via Docker

git clone [vista repo]
cd vista
docker build --rm -t vista .
cd ~/my_fasta_dir
docker run --rm -v $PWD:/tmp vista /tmp/my_vibrio_genome.fasta > result.json

Running directly

First install NCBI-BLAST (blastn & makeblastdb), python 3 and pip.

git clone [vista repo]
cd vista
pip3 install -r requirements.txt
python3 vista.py build
python3 vista.py search /path/to/my_vibrio_genome.fasta > result.json

Example output

{
    "virulenceGenes": [
        {
            "name": "ctxA",
            "type": "Toxin",
            "status": "Present",
            "matches": [
                {
                    "contigId": ".CNRVC970056_CATTTT_L002.23",
                    "queryStart": 3385,
                    "queryEnd": 4161,
                    "refStart": 1,
                    "refEnd": 777,
                    "frame": 1,
                    "isForward": true,
                    "isComplete": true,
                    "isDisrupted": false,
                    "isExact": true,
                    "identity": 100.0
                }
            ]
        },
        ... etc ...
    ],
    "virulenceClusters": [
        {
            "name": "TCP cluster",
            "type": "colonisation",
            "genes": [
                "tcpA",
                "tcpB",
                "tcpC",
                "tcpD",
                "tcpE",
                "tcpF",
                "tcpH",
                "tcpI",
                "tcpJ",
                "tcpN",
                "tcpQ",
                "tcpR",
                "tcpS",
                "tcpT"
            ],
            "id": "tcp",
            "matches": {...as above...},
            "present": [
                "tcpA",
                "tcpB",
                "tcpC",
                "tcpD",
                "tcpE",
                "tcpF",
                "tcpH",
                "tcpI",
                "tcpJ",
                "tcpN",
                "tcpQ",
                "tcpR",
                "tcpS",
                "tcpT"
            ],
            "missing": [],
            "incomplete": [],
            "status": "Present"
        },
        ...etc...
    ],
    "serogroup": "O1",
    "serogroupMarkers": [
        {
            "gene": "rfbV",
            "name": "O1",
            "matches": [...as above...]
        },
        {
            "gene": "wbfZ",
            "name": "O139",
            "matches": [...as above...]
        }
    ],
    "biotype": "O1 El Tor",
    "biotypeMarkers": [
        {
            "name": "O1",
            "gene": "rfbV",
            "matches": [...as above...]
        },
        {
            "name": "O1 El Tor",
            "gene": "ctxB3",
            "matches": [...as above...]
        }
    ]
}

Acknowledgements

Originally developed by Corin Yeats and Sina Beier as part of the Vibriowatch project between the Centre for Pathogen Genome Surveillance, Big Data Institute, Oxford and Nick Thompson's team at the Wellcome Sanger Institute. We would like to acknowledge the support of our hosting institutes.

Contributors

Corin Yeats
Sina Beier
Avril Coghlan
Nick Thompson
David Aanensen

Licensing

See LICENSE.

pathogenwatch-oss/vista