A local transcriptome assembler for SNPs, indels and AS events

Latest News

  • 2021-03-31: KisSplice2RefGenome version 2.0.1 Release.
    Will now keep only one of any number of duplicated events.
  • 2021-03-08: KisSplice version 2.5.4 Release.
    Fix bug with new version of gcc (gcc10).
  • 2020-07-02: KisSplice2RefGenome version 2.0.0 Release.
    Output revised and clarified. Now facilitates downstream analysis in IGV.
  • 2020-04-06: KisSplice version 2.5.0 Release.
    Now includes bcalm ( major speedup, lower memory footprint for graph construction.
  • 2018-03-09: Our SR paper on assembly-first analysis of alternative splicing is published. Full protocol to reproduce the results is available here. Video (in french) explaining the work is available here.
  • 2018-02-21: KissDE is now on Bioconductor
  • 2017-02-28: Our AMB paper is published. We show that controlling the number of branching k-mers improves both local and global transcriptome assemblers
  • 2016-07-31: Our NAR paper is published. Full protocol to reproduce the results is available here


KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

KisSplice + Which type of data do I have?
Which post-treatment can I use?
I have a reference genome KisSplice2refgenome differential analysis: kissDE
I have no reference genome KisSplice2refTranscriptome

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