RepeatExplorer
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