Plant Molecular and Cellular

Growing sequencing and assembly efforts have been met by the advances in high throughput machines. However, the presence of massive amounts of repeats and transposons complicates the as-sembly process. Given a library of possible repeats, this paper considers the problem of identifying repeats and transposons in the fragments (also called reads) generated from sequencing machines. This is a difficult problem as the locations of the fragments on the complete genome are not known. Furthermore, due to insertion, deletion and other evolutionary factors, different copies of repeats can diverge from each other. The presence of transposons, (also called jumping genes) makes the problem even harder as they can split other repeats and make them diverge from the actual repeats. We develop a graph based method named RepFrag which can efficiently identify repeats in a given set of fragments. We firs