This website provides information and documentation about RepeatExplorer programs, a computational tools which includes utilities for graph-based clustering and characterization of repetitive sequences in next-generation sequencing data and tools for the detection of transposable element protein coding domains.

galaxy_public         manual         bitbucket


The 7th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis will be held in Institute of Plant Molecular Biology, České Budějovice, Czech Republic on May 22-24, 2018. Registration for workshop is now open.


  • RepeatExplorer programs are available for public on our Galaxy server. This server is provided within Elixir CZ project and is maintained by CESNET and CERIT-SC that are participants of this project.
  • Source code programs included in RepeatExplorer is available from bitbucket repository and can be used to run repeat analysis from command line interface.
  • TAndem REpeat ANalyzer –TAREAN – is a computational tool for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported. TAREAN is available as part of RepeatExplorer2 pipeline.
  • Original version of RepeatExplorer is available on our old galaxy server repeatexplorer.umbr.cas.cz, source code can be obtained from bitbucket. This version of RepeatExplorer is no longer actively developed.

RepeatExplorer pipeline is developed and maintained by the Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Biology Centre AS CR, Ceske Budejovice, Czech Republic