ReRep: Reads and Repeats

ReRep is an implementation of a methodology to find repeats in genome survey sequence (GSS) data. It can be applied in low coverage GSS data of a partial sequenced genome to detect and annotate repeats. Or to mask repeats in a genome assembly. Its strength compared to genome assembly programs is the variability of the parameters, detection of more distant members of a repeat family and an early estimate and overview of the repeats.

ReRep is programmed in PERL and was tested in Linux environments. It depends on following third party packages:
MUMmer (download) and / or BLAST
CAP3 (download)
GD (for graph output), (download) - the GD::Graph::lines module

ReRep has been accepted for publication
BMC Bioinformatics. 2008 Sep 9;9:366.

ReRep can be DOWNLOADED and used freely for scientific purposes. In the tar ball, a readme file explains the necessary steps to install and run the program.

Further in the tar ball included is a test data set of around 1000 reads of a GSS project of the Leishmania braziliensis genome.