Commit 63b4c232 authored by Mathieu Giraud's avatar Mathieu Giraud

doc: main README.org, the Vidjil components

parent cc433be7
#+TITLE: Vidjil -- V(D)J recombinations analysis
#+AUTHOR: The Vidjil team (Mathieu, Mikaël and Marc)
# 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.
Vidjil process high-througput sequencing data to *extract V(D)J
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
to output the most abundant clones. Vidjil can also clusterize similar
clones, or leave this to the user after a manual review.
Vidjil also contains a *dynamic browser* for visualization and
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
the algorithmic component of Vidjil or by other V(D)J analysis
pipelines.
Finally, a *server* is currently developed to link the browser and the
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]]
** The server
- 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.
The development code is available on [[http://www.github.com/magiraud/vidjil]].
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]]
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