title: KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
abstract: BACKGROUND
  In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then introduce an exact algorithm, called KISSPLICE, to extract alternative splicing events.
  
  
  RESULTS
  We show that KISSPLICE enables to identify more correct events than general purpose transcriptome assemblers. Additionally, on a 71 M reads dataset from human brain and liver tissues, KISSPLICE identified 3497 alternative splicing events, out of which 56% are not present in the annotations, which confirms recent estimates showing that the complexity of alternative splicing has been largely underestimated so far.
  
  
  CONCLUSIONS
  We propose new models and algorithms for the detection of polymorphism in RNA-seq data. This opens the way to a new kind of studies on large HTS RNA-seq datasets, where the focus is not the global reconstruction of full-length transcripts, but local assembly of polymorphic regions. KISSPLICE is available for download at http://alcovna.genouest.org/kissplice/.
authors.affiliation: INRIA Grenoble Rhône-Alpes, France.
authors.forename: Gustavo A T
authors.initials: GA
authors.lastname: Sacomoto
authors.forename: Janice
authors.initials: J
authors.lastname: Kielbassa
authors.forename: Rayan
authors.initials: R
authors.lastname: Chikhi
authors.forename: Raluca
authors.initials: R
authors.lastname: Uricaru
authors.forename: Pavlos
authors.initials: P
authors.lastname: Antoniou
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
authors.forename: Pierre
authors.initials: P
authors.lastname: Peterlongo
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacroix
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D016678:Genome; D006801:Humans; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D012015:Reference Standards; D017423:Sequence Analysis, RNA; D020080:Tandem Repeat Sequences; D059467:Transcriptome