What's new?

See you at JOBIM and GCC

CRAC has a poster at the Galaxy Community Conference in Oslo, Norway. CRAC was also presented today at the french JOBIM conference. You can see the slides here.

CRAC version 1.3.0 released

A new version of CRAC is released.

Among the main changes:

  • SAM format is now compliant with Picard tools
  • CRAC is now able to produce gzip-compressed output files (use --gz option) — thanks to Linlin Yan for asking
  • CRAC is now built with libraries embedded by default (thanks to Sarah Pohl for pointing that out)
  • Several bugs have been fixed regarding problems related to CIGAR string in SAM output (thanks to Linlin Yan for reporting one of them).

CRAC mentioned in Nature

Nature wrote about CRAC in the  Research Highlights section of its May 2 issue.

Just a tiny mistake: all the authors are not from Montpellier and are not part of Eric's team ;)

CRAC version 1.2.4 released

CRAC is now released under version 1.2.4. It integrates several improvements:

Bug corrections :

  • Bug #15605 solved (segfault on very specific read), on both strands
  • Bug #15630 corrected: range in the BWT was not properly initialized with revcomp
  • FM-Index: Bug solved with genome length multiple of 64.
  • Update headers for paired-end-chimera crac homemade file.
  • Correct several bugs in CRAC emt :
    • Fix multi-threading
    • Added FASTA support


  • CRAC is now using gkArrays 2.0.3
  • New algorithm for chimera validation using paired-end reads.
    We had miss some cases in the process of validating chimera junctions with paired-end reads.
  • Add unit tests in CRAC :
    Every bug solved is now included as a unit test to avoid regression.
  • Add XR field in SAM output for information relative to the read (p_loc and p_support are now under the XR field

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

CRAC version 1.2.3 released

CRAC is now released under version 1.2.3. It integrates several improvements:

Correction of several bugs:

  • Correct --all argument. No paired-end-chimera is created if we are not using paired-end reads
  • Bug #15605 corrected (segmentation fault in FM-index, when a range was at the top of the BWT, but then becomes empty)
  • Deletion position was indicated one position before where it should be
  • Correct the k-mer verification test in stringent-chimera. The test to determine if the kmer used for verification wasn't in a break was based on support profile instead of location profile.

Add several improvements:

  • Add some unit tests 
  • Use version 2.0.2 of Gk-arrays

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

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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