SplitSeek is a program for de novo prediction of splice junctions in RNA-seq data. It is based on a split read alignment where the reads are split into two parts that are mapped separately. The alignments are then processed by the SplitSeek software through a number of analysis steps. The result is a list of predicted splice junctions which can be viewed in the UCSC genome browser. This method can also be applied to search for genomic rearrangements such as small insertions and deletions.

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For a more detailed description of SplitSeek, please see:

Ameur A, Wetterbom A, Feuk L, Gyllensten U. Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol. 2010 Mar 17;11(3):R34. 


This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.


  • SplitSeek user manual.
  • The split read alignment is done using the AB WT pipeline (Pre-Bioscope version). It can be downloaded here.

Software Download

  • The current version of the SplitSeek program can be downloaded here.


This program is developed at the Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.

Bug reports and questions regarding the SplitSeek implementation can be emailed to Adam Ameur. 

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