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