Discover repeats in your next generation sequencing data (original) (raw)

RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering (Novak et al. 2010) of sequence reads to identify repetitive elements and a number of additional programs that aid in their annotation and quantification (Novak et al. 2013).

Availability

• RepeatExplorer programs can be run on our public Galaxy server. The server is provided within Elixir CZ project and is maintained by its partners CESNET and CERIT-SC.
• The source code of the programs included in RepeatExplorer is available from bitbucket repository and can be used to run the repeat analysis from the command-line interface.
• TAndem REpeat ANalyzer –TAREAN – is a computational tool for unsupervised identification of satellite repeats from unassembled sequence reads (Novak et al. 2017). 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.
• The previous version of RepeatExplorer is available on our old galaxy server repeatexplorer.umbr.cas.cz, its source code can be obtained from bitbucket. This version of RepeatExplorer is no longer actively developed.
• Virtualbox image

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