Repetitive elements comprise large proportion of many genomes. They have impact on both genome evolution and regulation. Their classification and the study of evolutionary history is a major emerging field. Various software exist to-date to classify and map repeats across genomes. The major unresolved drawback, however, is the fragmented nature of many identified repeat loci. This ultimately makes the classification of novel repeats and their evolutionary analyses difficult. To improve on this, we developed a pipeline (RepeatCraft) that integrates results from several repeat element classification tools based on both sequence similarity and structural features. The pipeline de-fragments closely spaced repeat loci in the genomes, reconstructing longer copies, thus allowing for a better annotation and sequence comparisons. The pipeline also includes a user interface that can run in a web browser allowing for an easy access and exploration of the repeat data.