RNA-Seq read analysis

CRAC proposes a novel way of analyzing reads that integrates genomic locations and local coverage, and delivers all above mentioned predictions in a single step. CRAC uses a double k-mer profiling approach to detect candidate mutations, indels, splice or fusion junctions in each single read.


download and installation instructions

CRAC is released under a CECiLL licence (a GPL-compliant licence).

CRAC relies on a read indexing approach, that is available independently from CRAC. This index, called Gk-arrays, can also be downloaded for being used with other software tools.


Philippe N. and Salson M. and Commes T. and Rivals E.
CRAC: an integrated approach to the analysis of RNA-seq reads
Genome Biology 14, 2013

Philippe N. and Salson M. and Lecroq T. and Léonard M. and Commes T. and Rivals E.
Querying large read collections in main memory : a versatile data structure
BMC Bioinformatics 12:242, 2011