REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.

ABSTRACT: Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply

SUBMITTER: Chu C 

PROVIDER: S-EPMC4792456 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature