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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 -- [[]]
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# Copyright (C) 2011-2016 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
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# [[]]

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 [[][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. 

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

* Vidjil components

** The algorithm

- Stable releases can be downloaded from
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- Development code is under [[algo/]]
- Documentation: [[doc/]]

** The browser and the patient database

- Access at (demo login: demo@vidjil, password: vidjil)
- Please contact us if you would like to test your data and have a full account on the web server
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- Development code is under [[browser/]] and [[server/]]
- Documentation (in progress): [[doc/]] and [[doc/]]
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* Code and license

Vidjil is open-source, released under GNU GPLv3 license. 
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You are welcome to redistribute it under [[][certain conditions]]. 
This software is for research use only and comes with no warranty.

The development code is available on [[]].
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Bug reports, issues and patches are welcome.

* The Vidjil team

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Vidjil is developed by [[][Mathieu Giraud]], Ryan Herbert, Tatiana Rocher and  [[][Mikaël Salson]]
from the [[][Bonsai bioinformatics team]] (CRIStAL, CNRS, U. Lille, Inria Lille).
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Vidjil is also developed by external colleagues:
Marc Duez located in Bristol (School of Social and Community Medicine, University of Bristol)
and Florian Thonier located in Paris (department of hematology, Necker hospital)
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Vidjil is developed in collaboration with 
the [[][department of Hematology]] of CHRU Lille, 
the [[][Functional and Structural Genomic Platform]] (U. Lille 2, IFR-114, IRCL), 
and the [[][EuroClonality-NGS]] working group.
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The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), by Région Nord-Pas-de-Calais (ABILES) and by Inria.

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* References
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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 

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You may also be interested in the following publication for the diagnosis of
acute lymphoblastic leukemia with high-throughput sequencing:

Yann Ferret, Aurélie Caillault, et al., “Multi-loci diagnosis of acute
lymphoblastic leukaemia with high-throughput sequencing and bioinformatics
analysis”, British Journal of Haematology 2016