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## Vidjil – Documentation
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)*

**[Vidjil](http://www.vidjil.org) is an open-source platform for the analysis of high-throughput
sequencing data from lymphocytes.** [V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are
essential for immunological diversity. They are also useful markers of
pathologies, and in leukemia, are used to quantify the minimal residual
disease during patient follow-up. High-throughput sequencing (NGS/HTS) now
enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html)
methods and software.

### Web application, user documentation

  - Tutorial "Mastering the Vidjil web application": [english](./tutorial/mastering-vidjil.html) ([pdf](./tutorial/mastering-vidjil.pdf)), [français](./tutorial/mastering-vidjil-fr.html)
    ([pdf](./tutorial/mastering-vidjil-fr.pdf)). Start by this tutorial to have an overview of Vidjil.
  - Web application [user manual](user.md)
  - [Demo access](http://app.vidjil.org/) to the patient, experiment and sample server
  - [Public datasets](http://www.vidjil.org/data/) supporting Vidjil publications

### Algorithm, web application, server, developper documentation

  - [Vidjil-algo documentation](vidjil-algo.md)
  - [Encoding clones with V(D)J recombinations](vidjil-format.md), specification of the `.vidjil` file format
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  - [Docker/Server installation and maintenance](server.md)
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These documentations and additional developer and maintainer documentation
are availaible from the [doc/](http://gitlab.vidjil.org/tree/master/doc) directory in the source files.

### Further help

Further help can always be asked to <contact@vidjil.org>. We can also arrange
phone or video meeting.