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From March 2013, a new webpage is dedicated to the KisSplice software:

Description and possible usages

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.


Downloading kisSplice imposes the full acceptance of the CeCILL license.

Most recent version for download (source code) : kisSplice-1.7.1.

And, pre-compiled binaries: kisSplice-1.7.1(MAC OSX 64bits) and kisSplice_1.7.1(LINUX 64bits).


User Guide


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

Mailing List

Please send an empty email to with the following title: subscribe Your_first_name Your_family_name


  • [18/12/2012] kisSplice_1.7.1
    • BUG: kissplice was crashing while parsing some fastq files.
    • Added new command line option to specify the k-mer count cutoff.
  • [27/07/2012] kisSplice_1.7.0
    • Python script kissplice replaces shell script
    • KisSplice can now be run in parallel mode
    • Fastq input is now supported, but qualities are not currently used
    • New option to keep the unfinished bccs
    • New quantification: Kissreads now outputs the total number of reads covering a path, and the number of reads per nucleotide. A read is said to cover a path if it overlaps with at least k nt (instead of 25 in the previous versions)
    • A bubble is read coherent if each nt is covered by at least one read (instead of 2).
    • Kissreads is now more memory efficient
    • Lighter graph representation
    • Faster duplicate cleaning procedure
    • BUG: duplicated edges in the DBG (not affecting the results) are now removed
    • BUG: kissreads not working on mac os x
    • BUG: clean_duplicates keeping some duplicate bubbles
    • BUG: wrong hamming distance calculation, causing event miss classification
  • [04/04/2012] kisSplice_1.6.3
    • Bug related to mac OS fixed
  • [29/03/2012] kisSplice_1.6.2
  • [14/02/2012] kisSplice_1.6
    • Possibility to chose the output directory (-o)
    • Possibility to run kissplice from any directory
    • Possibility to avoid the computation of SNPs and sequencing errors (-s)
    • Updated manual
  • [03/02/2012] kisSplice_1.5.1 Small bug fixed
  • [23/01/2012] kisSplice_1.5
    • ranking and sorting results on read coverage and not k-mer coverage
    • provides 5 files:
      * uncoherent (a bit useless)
      * Type 0: SNPS / sequencing errors
      * Type 1: splicing events
      * Type 2: Tandem repeats
      * Type 3: Short indels
  • [17/01/2012] Possibility to use k larger than 32 nt (slower) or smaller than 32 (faster) kisSplice_1.3
  • [16/01/2012] kisSplice_1.2
    • Better de-bruijn graph creation
    • Read length unlimited
    • Checks the read coherency and provides read coverage on results
  • [28/10/2011] Fixed small bugs, improved the user guide. : kisSplice_1.1
  • [24/10/2011] First release:kisSplice_1.0