RepeatExplorer

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Description

RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify repetitive elements within analyzed samples. The analysis principles were described in Novak et al. (2010) and examples of its application can be found in a number of published papers (see Appendix). It should be noted that although the repeat identification algorithm generally works for any genome, some parts of the pipeline (e.g. protein domain-based classification of mobile elements) were primarily developed for application to plant genomics. However, there is a possibility to supply a custom repeat database to improve sensitivity in classification of non-plant repeats.

License

GNU GPL version 3

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of repeatexplorer and load default version of repeatexplorer as

module avail repeatexplorer/ # list available modules
module load repeatexplorer   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail repeatexplorer

and choose explicit version you want to use.

Galaxy portal https://galaxy-elixir.cerit-sc.cz/ (wiki https://wiki.metacentrum.cz/wiki/Galaxy ) Script version from the portal

module add repeatexplorerREportal
seqclust_cmd.py -h

Older script version:

module add repeatexplorer
seqclust_cmd.py -h

Documentation

http://repeatexplorer.umbr.cas.cz/static/html/help/manual.html

Papers about RE: http://www.biomedcentral.com/1471-2105/11/378 and http://bioinformatics.oxfordjournals.org/content/29/6/792

Homepage

http://repeatexplorer.umbr.cas.cz/