Vibriowatch
Vibriowatch is a PathogenWatch database for V. cholerae. Vibriowatch contains >6000 published V. cholerae genomes, and manually-curated metadata from the literature such as place, date and source of isolation; and phenotypic data such as serogroup and antimicrobial resistance.
Vibriowatch is aimed for use by clinicians and public health workers studying cholera outbreaks, as well as for research biologists investigating V. cholerae.
Given raw genome sequencing reads, or a genome assembly for a bacterial isolate, key questions that can be answered using Vibriowatch include (click on the links below for a short guide for those in a hurry):
Does my isolate belong to the current pandemic lineage of Vibrio cholerae?
What is the predicted antimicrobial resistance profile of my isolate?
Is my isolate closely related to other sequenced Vibrio cholerae isolates?
In this tutorial we’ll introduce the V. cholerae genomic data; explain how you can upload your own sequencing reads or genome assembly to Vibriowatch; and tell you about bioinformatics analyses you can carry out in Vibriowatch of your isolates and existing V. cholerae genomes in Vibriowatch. The table of contents is below, or to the left.
Vibriowatch is funded by the Bill and Melinda Gates Foundation and is a collaboration between the Thomson group at the Wellcome Sanger Institute and the Centre for Genomic Pathogen Surveillance).
Contact
I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk
Contents
- Vibrio cholerae genomic data
- Navigating Vibriowatch
- How to search for an isolate in Vibriowatch and see its report page
- How to make a collection of isolates in Vibriowatch
- Finding your list of collections in Vibriowatch
- Public collections in Vibriowatch
- Exploring the timeline for a collection of isolates
- Exploring the tree for a collection of isolates
- Displaying metadata on the tree for a collection of isolates
- Contact
- Assemblies and assembly quality
- Short guide for those in a hurry: is my isolate Vibrio cholerae?
- Check if your fastq files of reads are suitable for Vibriowatch
- Upload reads to Vibriowatch, to make an assembly
- Upload an assembly for an isolate
- Verify that your isolate is Vibrio cholerae
- View the Vibriowatch report page for your isolate
- View the assembly statistics for your isolate
- Download the assembly for your isolate
- Run CheckM to check if the assembly for your isolate is contaminated
- Contact
- Vibrio cholerae lineage information
- Short guide for those in a hurry: does my isolate belong to the current pandemic lineage?
- What is known about Vibrio cholerae lineages?
- What is MLST?
- How to view MLST information for your isolate
- What is PopPUNK?
- How to view PopPUNK information for your isolate
- Build a tree to check if your isolate belongs to the pandemic lineage: example 1
- Build a tree to check if your isolate belongs to the pandemic lineage: example 2
- Build a tree to check if your isolate belongs to the pandemic lineage: example 3
- Contact
- Finding closely related isolates
- Short guide for those in a hurry: is my isolate closely related to other sequenced Vibrio cholerae isolates?
- Use cgMLST to find close relatives of your isolate: example 1
- Use cgMLST to find close relatives of your isolate: example 2
- Use cgMLST to find close relatives of your isolate: example 3
- Use cgMLST to find close relatives of your isolate: example 4
- Build a phylogenetic tree of your isolate and its closest relatives: example 1
- Build a phylogenetic tree of your isolate and its closest relatives: example 2
- Contact
- Predicting virulence genes
- Predicting antimicrobial resistance genes
- Short guide for those in a hurry: what is the predicted antimicrobial resistance profile of my isolate?
- Antimicrobials recommended for treating cholera
- Antimicrobial resistance in the current pandemic lineage of Vibrio cholerae
- Predicting antimicrobial resistance genes in your isolate, and assessing the predictions
- Displaying antimicrobial resistance gene presence/absence on the tree for a collection of isolates
- Contact
- Predicting plasmids
- Acknowledgements