KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

KISSPLICE is an algorithm for identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. KISSPLICE is based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads.

kisSplice calls splicing events from one to n sets of NGS/HTS reads. It takes as input one to n sets of NGS raw reads or an already created de-Bruijn graph. It first constructs the de-Bruijn graph if it is not provided and then detects all patterns in the de Bruijn graph which correspond to alternative splicing events.

KISSPLICE is available for download at http://alcovna.genouest.org/kissplice/

  • Sacomoto GA, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot MF, Peterlongo P, Lacroix V. (2012) KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics 13(Suppl 6), S5. [article]