What's new?

Galaxy wrapper released

Galaxy is « an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses ».

Marine Rohmer worked during her Master's on creating a Galaxy wrapper for CRAC. You can download it here. You may have to modify it to adapt it to your needs.

CRAC version 1.2.2 released

CRAC is now released under version 1.2.2. It integrates several improvements:

Correction of several bugs:

  • Bug #15576 with mandatory arguments between --server and -o arguments
  • Bug #15575 with segfault using -k argument
  • Bug #15540 (memory leak with deletions in sequence errors)
  • Bug #15352 that was due to a bad merge between 2097 and 2114 revisions of taginfo.cpp file
  • Bug #15579 (only show once support and localisation when --detailed-sam)
  • Correction of the Kmer verification test for paired reads and chimeras
  • Correct the samOutput for paired-end reads. The field Rnext was not properly filled and the flag was update with paired-end data after being written
  • Correct a segfault when using option --splice. We were trying to write in spliceNoCover as well
  • Correct a bug in repetition case and change condition to save the longest repetition
  • Correct a bug with --emt argument. Sequence was not properly reverse complemented in the sam output when the read was mapped to the reverse strand of the genome.
  • Correst a bug iwith --detailed-sam option: reverse the profile and localisation in detailed-sam output when read is reversed.

Add several improvements:

  • A --no-ambiguity option in crac.cpp to increase accuracy in exchange for sensitivity
  • A new output file "pairedEndChimera", this file contains chimera between paired-end tags where junctions are not sequenced. A new parameter to use this file is available : --paired-end-chimera
  • Some unit tests for chimeras, the CIGAR chaine, SNVs


  • Change packaging to take account of the man page
  • Set cigar to * in sam when segment is unmapped
  • Update the text to display when using --version option
  • Update doc, add examples and add a specific documentation for homemade CRAC formats
  • Use the new version 2.0.1 of Gk-arrays

This changes were made by Jérôme Audoux, Nicolas Philippe and Mikaël Salson (in alphabetical order).

CRAC version 1.2.1 released

CRAC is now released under version 1.2.1. It integrates several improvements:

  • Paired-end integration for chimera detection
  • Better management of parallelization
  • Integration of chimera-stringent option
  • Management of strand-specific RNA-Seq reads
  • Many bug fixes, including an annoying one regarding the creation of the index
  • Added a --emt option for those wanting to map exactly (ie. without any difference) reads on a genome
  • Use the new version 2.0.0 of Gk-arrays

Thanks to Jérôme Audoux for several improvements as well as Nicolas Philippe and Mikaël Salson.

Article published

The article is now published in Genome Biology online. The final PDF version is not avaliable yet.

Article Accepted

The publication on CRAC has been accepted for publication in Genome Biology.

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News and updates

New releases and related tools will be announced through the CRAC mailing list.

Getting started

You want to try CRAC? Download it and check our getting started guide.


Check out the CracTools : Integrated pipelines for RNA-Seq analysis using CRAC additional fields, annotation and much more.


A galaxy wrapper for CRAC is available and can be downloaded here.

Contact us

Any question regarding the software? Send an email to crac-bugs@lists.gforge.inria.fr.
A question, a comment, a remark on the algorithm or the article, send an email to crac-article@lists.gforge.inria.fr


Nicolas Philippe, Mikaël Salson, Thérèse Commes and Eric Rivals.CRAC: an integrated approach to the analysis of RNA-seq reads doi:10.1186/gb-2013-14-3-r30