README.org 4.6 KB
Newer Older
1 2 3
#+TITLE: Vidjil -- V(D)J recombinations analysis
#+AUTHOR: The Vidjil team (Mathieu, Mikaël and Marc)

4 5 6
[[https://travis-ci.org/vidjil/vidjil][http://img.shields.io/travis/vidjil/vidjil.svg]]
[[http://opensource.org/licenses/GPL-3.0][http://img.shields.io/badge/license-GPLv3+-green.svg]]
[[https://coveralls.io/r/vidjil/vidjil][http://img.shields.io/coveralls/vidjil/vidjil.svg]]
7

8
# Vidjil -- V(D)J recombinations analysis -- [[http://www.vidjil.org]]
Mikaël Salson's avatar
Mikaël Salson committed
9
# Copyright (C) 2011-2016 by Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
10 11 12 13 14 15 16 17 18
# [[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.

19 20
The Vidjil platform contains three components. The Vidjil algorithm
process high-througput sequencing data to *extract V(D)J
21 22 23
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
24 25 26
to output all sequenced clones. The analysis is extremely fast
because, in the first phase, no alignment is performed with database
germline sequences. 
27

28
The Vidjil *dynamic browser* is made for the visualization and
29 30
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
31 32 33
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.
34

35 36
Finally, a *patient database* with a server
is currently developed to link the browser and the
37 38 39 40 41 42 43 44
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

45
- Stable releases can be downloaded from http://bioinfo.lille.inria.fr/vidjil
46 47 48
- Development code is under [[algo/]]
- Documentation: [[doc/algo.org]]

49
** The browser and the patient database
50

51
- Access at http://rbx.vidjil.org/browser (demo login: demo@vidjil, password: vidjil)
52
- Please contact us if you would like to test your data and have a full account on the web server
53 54
- Development code is under [[browser/]] and [[server/]]
- Documentation (in progress): [[doc/browser.org]] and [[doc/server.org]]
55 56 57 58

* Code and license

Vidjil is open-source, released under GNU GPLv3 license. 
Mathieu Giraud's avatar
Mathieu Giraud committed
59 60 61 62
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/]].
63 64 65 66
Bug reports, issues and patches are welcome.

* The Vidjil team

Mikaël Salson's avatar
Mikaël Salson committed
67
Vidjil is developed by [[http://cristal.univ-lille.fr/~giraud][Mathieu Giraud]], Ryan Herbert, Tatiana Rocher and  [[http://cristal.univ-lille.fr/~salson][Mikaël Salson]]
68
from the [[http://cristal.univ-lille.fr/bonsai][Bonsai bioinformatics team]] (CRIStAL, CNRS, U. Lille, Inria Lille).
Mikaël Salson's avatar
Mikaël Salson committed
69 70 71
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)
72 73 74 75
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.
Mikaël Salson's avatar
Mikaël Salson committed
76
The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), by Région Nord-Pas-de-Calais (ABILES) and by Inria.
77

Mikaël Salson's avatar
Mikaël Salson committed
78
* References
79 80 81 82 83 84 85 86

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]]

Mikaël Salson's avatar
Mikaël Salson committed
87 88 89 90 91 92 93
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
http://dx.doi.org/10.1111/bjh.13981