Cholera genomics
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Welcome to our free online course on *Vibrio cholerae* genomics!

The aim of this course is to teach you about *V. cholerae* genomics, so that you can use genomics to perform analyses relevant to cholera public health, and extract meaningful insights from *V. cholerae* genomic data. 

This course includes all you want to know about sequencing and analyses of *V. cholerae* genomes, including advanced bioinformatics topics relevant to *V. cholerae* genomics (e.g. genome assembly, phylogenetics, predicting antimicrobial resistance, etc.). 

The course includes both theoretical material and bioinformatics teachings.

The course will teach how to carry out bioinformatics analyses using `Vibriowatch`_, as well as other bioinformatics tools.
If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our `Vibriowatch`_ tutorial.

.. _Vibriowatch: https://vibriowatch.readthedocs.io

Theoretical material in this course on topics relevant to *V. cholerae* genomics includes:

* The disease cholera and its epidemiology.
* The species *Vibrio cholerae*, and its geographic distribution. 
* The history of cholera, and the history of global spread of the current pandemic lineage of *V. cholerae* (the 7PET lineage).
* Suggested strategies for sample collection and sequencing of *V. cholerae*.
* Isolates, lineages and sublineages of *V. cholerae*, their geographic distribution and role in cholera and diarrhoeal illness.
* Principal features of the *V. cholerae* genome.
* Potentially misleading results from surveilling presence/absence of marker genes and molecular/biochemical tests alone, in the absence of whole-genome sequencing data.
* Sublineages of 7PET, their geographic distribution, spread, and genomic/phenotypic features, and emergence of novel genetic variants in 7PET.
* Pathogenesis of cholera and genetic determinants of virulence, including new variants of concern and variants of interest.
* Cholera treatment and use of antimicrobials.
* Spread of antimicrobial resistance within key lineages of *V. cholerae* (e.g. within the 7PET lineage), as well as within *V. cholerae*, and also between other species of bacteria and *V. cholerae*.
* How genomics can play a role in public health decisions for cholera, and the potential of genomics as a platform to further refine cholera control strategies (e.g. vaccination strategies).

In each topic, learning will be enriched by examples of *V. cholerae* genome analysis, and practical bioinformatics exercises for learners, with an emphasis on analysing cholera genome data for public health. 

Vibriowatch
-----------

In later modules of this course, you will learn how to carry out bioinformatics analyses using `Vibriowatch`_, as well as other bioinformatics tools.
If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our `Vibriowatch`_ tutorial.

.. _Vibriowatch: https://vibriowatch.readthedocs.io

Contact
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I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk

Acknowledgements
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Contributors to this course: Avril Coghlan, Matt Dorman, Ismail Bashir, Anne Bishop, Amber Barton, Stephanie McGimpsey, Jolynne Mokaya, Nisha Singh, Nick Thomson. 

Contents
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.. toctree::

   vibriogenomes
   vibriogenomes2
   vibriogenomes3
   vibriogenomes4
   vibriogenomes_glossary
   vibriogenomes_answers
   assemblies
   mlst
   closerelatives
   virulenceAMR