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Commit 3141981e authored by Mathieu Giraud's avatar Mathieu Giraud
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doc/vidjil-algo.md: put again first paragraphs, details

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# vidjil-algo – Command-line manual
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
V(D)J recombinations in lymphocytes are essential for immunological
Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire -- [[http://www.vidjil.org]]
Copyright (C) 2011-2018 by Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
This is the help of vidjil-algo, for command-line usage.
This manual can be browsed online:
- <http://www.vidjil.org/doc/algo> (last stable release)
- <http://git.vidjil.org/blob/master/doc/algo.md> (development version)
Other documentation (users and administrators of the web application, developpers) can be found from <http://www.vidjil.org/doc/>.
## About
*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.
......@@ -250,7 +269,7 @@ The `germline/*.g` presets configure the analyzed recombinations.
The following presets are provided:
- `germline/homo-sapiens.g`: Homo sapiens, TR (`TRA`, `TRB`, `TRG`, `TRD`) and Ig (`IGH`, `IGK`, `IGL`) locus,
including incomplete/unusal recombinations (`TRA+D`, `TRB+`, `TRD+`, `IGH+`, `IGK+`, see [locus.org](http://git.vidjil.org/blob/master/doc/locus.org))
including incomplete/unusal recombinations (`TRA+D`, `TRB+`, `TRD+`, `IGH+`, `IGK+`, see [locus](locus)).
- `germline/homo-sapiens-isotypes.g`: Homo sapiens heavy chain locus, looking for sequences with, on one side, IGHJ (or even IGHV) genes,
and, on the other side, an IGH constant chain.
- `germline/homo-sapiens-cd.g`: Homo sapiens, common CD genes (experimental, does not check for recombinations)
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