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.
Improvements
- 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