RepeatExplorer: Collection of Tools for Mining of Repetitive Elements from NGS Data

Recent availability of large amounts of sequencing data from next generation sequencing (NGS) unlocks numerous possibilities in genome exploration but also poses new challenges on data mining. Since repetitive DNA make up prevalent portions of both plant and animal genomes, NGS data are particularly convenient resource for analysis of genomic repeats. Here we present RepeatExplorer, a collection of software tools especially designed to characterize repetitive sequences from NGS data. RepeatExplorer implements graph-based clustering of sequence reads and provide de novo identification of repeats, classification and quantification. Typically, fraction of sequencing run counting several million reads which correspond to low depth coverage of eukaryotic genomes is sufficient to characterize majority of repeats found in genome including middle and high copy number elements.

RepeatExplorer is available to scientific community as stand alone Galaxy based server (www.repeatexplorer.org) with user friendly interface or alternatively as collection of command line scripts. It includes all necessary tools for short NGS read preprocessing, de-novo repeat identification, classification of repeats using public and custom repeat databases, investigation of phylogenetic relationship of retroelements, comparative analysis of multiple species and visualization of results.