What's new?

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). 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 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 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).

Tags : crac release

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.


Tags : crac poster slide conference

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 1.3.0 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 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).