A local transcriptome assembler for SNPs, indels and AS events

Latest News

  • 2018-01-30: Our paper on assembly-first analysis of alternative splicing is accepted in Scientific Reports. Full protocol to reproduce the results is available here
  • 2017-05-12: kissDE version 1.5.0 Release
  • 2017-02-28: Our AMB paper is out. We show that controlling the number of branching k-mers improves both local and global transcriptome assemblers
  • 2016-07-31: Our NAR paper is out. Full protocol to reproduce the results is available here
    Supplementary data is accessible here
  • 2016-04-14: KisSplice version 2.4.0-p1 Release


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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