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KisSplice | De-novo calling alternative splicing events from RNA-seq data

Detects variants such as single nucleotide polymorphisms (SNPs), indels and alternative splicing (AS) in transcriptomes. KisSplice is a standalone software able to identify bubble patterns generated by AS events without the need of a reference genome. The application can be used to census AS events in various species, however it is suited only for splicing not for the reconstruction of an entire transcript.

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KisSplice classification

KisSplice specifications

Unique identifier:
Command line interface
Input data:
A or some sets of reads, or a bi-directed de-Bruijn graph.
Operating system:
Unix/Linux, Mac OS
CeCILL version 2.1
Software type:
Restrictions to use:
Input format:
Programming languages:
C++, Python
Computer skills:

KisSplice distribution


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KisSplice support



  • Pierre Peterlongo <>
  • Vincent Lacroix <>
  • Leandro Lima <>


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Inria Grenoble, Montbonnot, France; CNRS, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France; IRISA Inria Rennes Bretagne Atlantique; GenScale Team, Université Rennes 1, Rennes, France

Funding source(s)

Supported by the Brazilian Ministry of Science, Technology and Innovation through the National Counsel of Technological and Scientific Development, under the Science Without Borders scholarship grant process number 203362/2014-4, the Agence Nationale de la Recherche ABS4NGS ANR project (ANR-11-BINF-0001-06) and Action n3.6 Plan Cancer 2009–2013, the Agence Nationale de la Recherche ANR-12-BS02-0008 (Colib’read), the European Research Council under the European Community’s Seventh Framework Programme (FP7 /2007–2013)/ERC Grant Agreement No. [247073]10.

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