As you know, CRAC is a RNA-Seq mapper which is able to identify splicing variants, chimeric events, indels and mutations at the read scale. Many people request us because, they need to:

  • aggregate reads associate to the same event
  • annotate events with a GFF/GTF file
  • combine the SAM/BAM file with another files (BAM vs BED, BED vs VCF, etc)

This is why, we have developed CracTools which are a complete toolbox designed to build pipelines on top of CRAC. CracTools are based on the “CracTools-core”, the key modules allowing to:

  • extract CRAC information using specific data structures, combine
  • extract BAM lines, BED lines and such using dedicated intervaltree structures
  • provide simply tools to extract CRAC features, combine different files, and count reads inside a region

Thereby, it is possible to use the “CracTools-core” in order to build more complex pipeline for RNA-Seq analysis such as chimCT dedicated to chimeras detection ro benchCT dedicated to RNA-Seq benchmarking.