Commit d5e4da5a authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: updates

parent be947880
#+TITLE: Vidjil -- Algo Manual
#+AUTHOR: The Vidjil team (Mathieu, Mikaël and Marc)
# Vidjil -- V(D)J recombinations analysis <http://bioinfo.lifl.fr/vidjil>
# 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.
Vidjil process high-througput sequencing data to extract V(D)J
junctions and gather them into clones. This analysis is based on a
seed heuristics and is fast and scalable because in the first phase, no
alignment is performed with database germline sequences. Vidjil starts
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
to output the most abundant clones. The analysis is extremly fast
because, in the first phase, no alignment is performed with database
germline sequences. Vidjil can also clusterize similar
clones, or leave this to the user after a manual review.
The method is described in the following paper:
......@@ -29,7 +28,6 @@ http://dx.doi.org/10.1186/1471-2164-15-409
Vidjil is open-source, released under GNU GPLv3 license.
* Supported platforms
Vidjil has been successfully tested on the following platforms :
......@@ -217,6 +215,6 @@ This file is used for the dynamic browser for visualization
and analysis of clones and their tracking along different samples,
(for example time points in a MRD setup or in a immunological study).
This application is currently in developpement and will be released in
Q4 2014. However, code source can be already accessed on
Q1 2015. However, code source can be already accessed on
http://www.vidjil.org/git. Please contact us (contact@vidjil.org) if
you would like to have an access on the web server.
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