crac - Package

CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
comparison to a reference genome. It is intended for transcriptomic
and genomic sequencing reads. More precisely, with transcriptomic
reads as input, it predicts point mutations, indels, splice junction,
and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
output positions and nature of sequence error that it detects in the
reads. CRAC uses a genome index. This index must be computed before
running the read analysis. For this sake, use the command "crac-index"
on your genome files. You can then process the reads using the command
crac. See the man page of CRAC (help file) by typing "man crac". CRAC
requires large amount of main memory on your computer. For processing
against the Human genome, say 50 million reads of 100 nucleotide each,
CRAC requires about 40 gigabytes of main memory. Check whether the
system of your computing server is equipped with sufficient amount of
memory before launching an analysis.  

crac - Source code

CRAC is freely available under a GPL-compliant CeCILL license. The
distribution comes as an archive (a gzipped tarball file .tar.gz)
containing the source code.

crac - Installation

1) Unpack the archive
2) Enter the directory crac-version-number
3) Type ./configure
4) If everything went fine, run make
5) You may want to check everything is ok by running make check
6) Finally, you can install the software on your system by running make install

If the configure step failed, that may be due to a missing library. In particular the zlib is needed. On a Debian or Debian-like system, you'll need to install zlib1g, zlib1g-dev.

After the compilation succeded you can find a more complete documentation 
inside the doc directory and a man page is also available.

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 Copyright © 2009-2011 -- LIRMM/CNRS
                          (Laboratoire d'Informatique, de Robotique et de
                          Microélectronique de Montpellier /
                          Centre National de la Recherche Scientifique)
                          LIFL/INRIA
                          (Laboratoire d'Informatique Fondamentale de
                          Lille / Institut National de Recherche en
                          Informatique et Automatique)
                          LITIS
                          (Laboratoire d'Informatique, du Traitement de
                          l'Information et des Systèmes).

 Copyright © 2011-2015 -- IRB/INSERM
                          (Institut de Recherches en Biothérapie /
                          Institut National de la Santé et de la Recherche
                          Médicale).

 Copyright © 2015-2016 -- AxLR/SATT
                          (Lanquedoc Roussilon/ 
			   Societe d'Acceleration de Transfert de Technologie).	  

 Programmeurs                                                               
      /Progammers: 
                   Nicolas PHILIPPE <nphilippe.resear@gmail.com>              
                   Mikaël SALSON    <mikael.salson@lifl.fr>
                   Jérôme Audoux    <jerome.audoux@gmail.com>                  
  with additional contribution for the packaging of:	                      
                   Alban MANCHERON  <alban.mancheron@lirmm.fr>               
                                                                             
  Contact:         CRAC list   <crac-bugs@lists.gforge.inria.fr> 
  Paper:           CRAC: An integrated RNA-Seq read analysis
                   Philippe N., Salson M., Commes T., Rivals E.
                   Genome Biology 2013; 14:R30.
 
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This File is part of the CRAC program.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.  This program is distributed in the
hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  See the GNU General Public License for more details.  You
should have received a copy of the GNU General Public License along
with this program.  If not, see <http://www.gnu.org/licenses/>.  
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Les commentaires sont les bienvenus/Comments are welcome.
