What's new?

CRAC version 2.0.0 released

We are happy to released new version of CRAC (V2), which comes with a lot of improvements, new options and bug corrections. This version is stable, better than ever, and ready for production use.


  • Memory impact divided by 10 on average (using libJellyfish)
  • Run time divided by 2 on average
  • Improvement of reads alignements (better precision and sensitivity)
  • Improvement of chimeric RNA predictions (based on a ML classifier)
  • Improvement of splice junction detection (using acceptor donor site signatures)
  • BAM output integration (using htslib)
  • The new CRAC summary file provides a partion of the mapped reads
  • NH field is consistent with the SAM recommendations

 New options

  • --rf,--fr,-ff to specify read orientation
  • --reads-index {GKARRAYS,JELLYFISH} to choose the datastructure used to index the read collection
  • --bam to output alignements directly encoded in BAM
  • --use-x-in-cigar to use X cigar operator for substitutions instead of M
  • --treat-mutiple <int> to provide multiple alignements for a given read (limited by the user choice)

 Bug corrections

  • Alignement extending outside the scope of chromosomes
  • CIGAR inconsistencies

New galaxy wrapper released!

Thanks to Y. Boursin and M.Deloger (http://deloger.blogspot.fr/), we are glad to release the new galaxy wrapper (v1.1) that is up to date with the latest version of CRAC (1.5). Note that the first wrapper was initiated by M. Rohmer (under the supervision of T. Commes, V. Lefort and A. Mancheron). A big thanks to them.

You can directly download it here.

If you have any trouble with the new wrapper, contact us at this address : crac-bugs@lists.gforge.inria.fr

CRAC distinguished

Nicolas Philippe has received a prize for his work on CRAC, recognized as a breakthrough in health and biology. The prize was given by the Pôle BIoSanté Rabelais.

CRAC version 1.5.0 released

Version 1.5.0 of CRAC is released. The main changes are the following ones:

  • Some bugs fixed llike inter compiler consistency, run with large reads file and bugs #16581, #16807, #16931, #17175 have been fixed.
  • Update SAM specification in order to be consistent with the last SAM version consistency (including chimeric aligments, extended fields, etc).
  • Display multiple alignments in SAM file for perfect hits.
  • Add an optional ProgressBar in order to check the progression of CRAC in batch mode.
  • Update the documentation, the sam specification and the man page.

CRAC version 1.3.2 released

Version 1.3.2 of CRAC is released. The main changes are the following ones:

  • Bug corrections affecting very large files in GkArrays (thanks a lot to Caroline Menguy for her help): processing very large files could take too many time (or even never finish).
  • A new option --treat-multiple has been added that allows to have information on all the reads in SAM file (by default CRAC doesn't care about reads that seem to appear too many times).
  • Output can be written on STDOUT using -o - and the summary can be written in a specific file using --summary.
  • Option --max-paired-length has been removed since its use is the same as for --max-splice-length. Please use the latter instead.
  • Few minor corrections (thanks to zhouwp for pointing out a problem with old version of grep, with make check).

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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