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.
It also outputs candidate SNPs and short indels (1 or 2nt). Longer indels (rare in RNAseq) are also output, but mixed with splicing events. For all categories, KisSplice outputs a quantification per condition. KISSPLICE is 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.
Developers 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/.
Reference:
Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix, KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics 2012, 13(Suppl 6):S5
Incoming search terms:
- KISSPLICE
- KISSPLICE paired-end reads
- splice mapper ngs
- rna seq methods
- rna seq de novo
- paired reads kissplice
- KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
- KISSPLICE: de-novo calling alternative splicing
- junction mapping ngs
- find alternative splicing sites from de novo RNA-seq
