CRAC is the only RNA-Seq mapping software that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in error detection method enabling high precison and sensitivity.
Find more about CRAC's concept here.

What's new?

CRAC version 2.5.0 released

 Bug corrections

  • Correct bug in chimeric alignment where alignments pos and chr where not properly setted
  • Correct memory leak detected with valgrind
  • Correct problem when second end has the length of the k-mer (Bug submitted by E. Mathijs)
  • Correct segfault problem producted by a very special case of chimeric alignments (Bug submitted by E. Mathijs)
  • Correct caninical k-mer counts from JellyReadsIndex when –stranded option is activated (Bug submitted by S. Beaumeunier)

CRAC version 2.4.0 released


  • integrate a better crac_score for chimera events detection
  • add a XS field as topHat does (it allows it to conform to cufflinks or stringtie)

 Bug corrections

  • extra fields are removed when the read is unmapped
  • XE inconsistencies for SNVs and indels
  • fixed wrong positions (reads and genome) for indels cases and add unit tests

CracTools version 1.2 released

If you love CRAC and you want to get the most out of it, take a look at the new version of the CracTools that is a complete toolbox designed to build pipelines (in Perl) on top of CRAC.

It is also shipped with a command-line tool that extracts splicing variants, chimeric variants, indels and SNPs identified by CRAC at the read level then collapses them into standard formats (BED,VCF).

CracTools logo

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 (, 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 :

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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
A question, a comment, a remark on the algorithm or the article, send an email to


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