A local transcriptome assembler for SNPs, indels and AS events


KisSplice can also be used when a reference (annotated) genome is available, in order to annotate the variants found and help prioritize cases to validate experimentally.
In this case, the results of KisSplice are mapped to the reference genome, using for instance STAR, and the mapping results are analysed using KisSplice2RefGenome.
Ultimately, for each variant, KisSplice2RefGenome outputs : a gene name, the type of event, CDS/UTR/intergenic, frameshift?, deltaPSI... and other technical features which may be useful for automatic post-treatment.
By default, the results are ranked by decreasing deltaPSI.
A short tutorial explaing how to run KisSplice, STAR and KisSplice2refGenome is available here
The full protocol from our SR paper is available here

Version 2.0.5 and above

kissplice2refgenome is now on Git! (2022-03-22)


  • Bug correction with --counts option.

Version 2.0.4

kissplice2refgenome version 2.0.4 (2022-02-24)


  • Bug correction concerning "X_gene_segment" lines in GFF3 files.

Version 2.0.3

kissplice2refgenome version 2.0.3 (2022-02-21)


  • * Major duplicated events removal update
  • * Major annotation file reading update
  • * Minor improvements and corrections

Version 2.0.2

kissplice2refgenome version 2.0.2 (2022-01-24)


  • Work with a wider range of GTF/GFF/GFF3 files.

Version 2.0.1

kissplice2refgenome version 2.0.1 (2021-03-31)


  • Keep only one of any number of duplicated events

Version 2.0.0

kissplice2refgenome version 2.0.0 (2020-07-02)


This is a major update:

  • Classification of events was updated and refined
  • Now outputs 7 .tsv files. One recapitulating all events. Others further describing : exact repeats, inexact repeats, other repeats, unmapped events and type2missedByKisSplice
  • Option to output a .gtf file, to visualise events for instance in IGV. The list of annotated transcripts supporting each variant is also output. THis is useful to outline novel variants.
  • Option to output a .sam file, to visualise events quantitatively in IGV.
  • Major speedup

Version 1.2.3

kissplice2refgenome version 1.2.3 (2019-08-27)
User's guide


This is a bug-fixing update:

  • The number of annotated splices sites was not correctly reported for the following event types: Intron Retention, Insertion and Deletion

Version 1.2.2

kissplice2refgenome version 1.2.2 (2019-07-20)
User's guide


This is a bug-fixing update:

  • The CDS column is now correctly reported if the AS event is located within the CDS of a gene. This is useful for prioritising candidates;

Version 1.2.1

kissplice2refgenome version 1.2.1 (2018-08-20)
User's guide


This is a bug-fixing update:

  • Corrected the parsing of the CIGAR string in unmapped events;

Version 1.2.0

kissplice2refgenome version 1.2.0 (2018-07-13)
User's guide


This is a bug-fixing update:

  • Corrected the bubble clustering;

Version 1.1.0

kissplice2refgenome version 1.1.0 (2018-04-10)
User's guide


This is a bug-fixing/performance update:

  • More precise event calling;
  • Corrected a bug with the strand column;
  • Improved performance.

Version 1.0.0

kissplice2refgenome version 1.0.0 (2015-05-11)
User's guide


KisSplice2refgenome requires Python 2.7.x and works on Linux systems. It requires

It is necessary to have as an input a file coming from the mapping of KisSplice results against a reference genome. KisSplice2refgenome allows .psl and .sam formats. For annotation files, .gtf is accepted.

Using kissplice2refgenome

You have access to all options description with the help command :

kissplice2refgenome -h

A first and very simple way to use KisSplice2refgenome is to input only the mapping file (psl or sam). An annotation (gtf) can also be added.

kissplice2refgenome <MAPPING_OUTPUT> -a [AnnotationFile] -o [PathToWriteOutput]