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#+TITLE: Vidjil -- V(D)J recombinations analysis
#+AUTHOR: The Vidjil team (Mathieu, Mikaël and Marc)

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# Vidjil -- V(D)J recombinations analysis -- [[http://www.vidjil.org]]
# Copyright (C) 2011, 2012, 2013, 2014 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
# [[contact@vidjil.org]]

V(D)J recombinations 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 [[http://omictools.com/rep-seq-c424-p1.html][Rep-Seq]] methods and softwares.

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The Vidjil platform contains three components. The Vidjil algorithm
process high-througput sequencing data to *extract V(D)J
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junctions and gather them into clones*. Vidjil starts 
from a set of reads and detects "windows" overlapping the actual CDR3.
This is based on an fast and reliable seed-based heuristic and allows
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to output all sequenced clones. The analysis is extremely fast
because, in the first phase, no alignment is performed with database
germline sequences. 
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The Vidjil *dynamic browser* is made for the visualization and
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analysis of clones and their tracking along the time in a MRD setup or
in a immunological study. The browser can visualize data processed by
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the Vidjil algorithm or by other V(D)J analysis pipelines.
The browser enables to explore further cluterings proposed
by software and/or done manually done by the user.
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Finally, a *patient database* with a server
is currently developed to link the browser and the
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algorithmic part. The goal is that the clinicians will be able to
upload, manage and process their runs directly on the browser (with
authentication).

* Vidjil components

** The algorithm

- Stable releases can be downloaded from http://www.vidjil.org/
- Development code is under [[algo/]]
- Documentation: [[doc/algo.org]]

** The browser

- Access at http://www.vidjil.org/browser (demo login: vidjil, password: vidjil, then select sample/L2-LIL.data in the file menu).
- Please contact us if you would like to test your data and have a full account on the web server
- Development code is under [[browser/]]
- Documentation (in progress): [[doc/browser.org]]

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** The server and the patient database
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- Currently under development, code is in [[server/]]
- Planned first release: Q1 2015
- Documentation (in progress): [[doc/server.org]]

* Code and license

Vidjil is open-source, released under GNU GPLv3 license. 
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You are welcome to redistribute it under [[http://git.vidjil.org/blob/master/doc/LICENSE][certain conditions]]. 
This software is for research use only and comes with no warranty.

The development code is available on [[http://git.vidjil.org/]].
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Bug reports, issues and patches are welcome.

* The Vidjil team

Vidjil is developed by Marc Duez, [[http://www.lifl.fr/~giraud][Mathieu Giraud]] and [[http://www.lifl.fr/~salson][Mikaël Salson]]
from the [[http://www.lifl.fr/bonsai][Bonsai bioinformatics team]] (LIFL, CNRS, U. Lille 1, Inria Lille).
Vidjil is developed in collaboration with 
the [[http://biologiepathologie.chru-lille.fr/organisation-fbp/91210.html][department of Hematology]] of CHRU Lille, 
the [[http://www.ircl.org/plate-forme-genomique.html][Functional and Structural Genomic Platform]] (U. Lille 2, IFR-114, IRCL), 
and the [[http://www.euroclonality.org/][EuroClonality-NGS]] working group.
The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041) and by Région Nord-Pas-de-Calais (ABILES). 

* Reference

If you use Vidjil for your research, please cite the following reference:

Mathieu Giraud, Mikaël Salson, et al.,
“Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing”,
BMC Genomics 2014, 15:409 
[[http://dx.doi.org/10.1186/1471-2164-15-409]]