An improved approach for reconstructing consensus repeats from short sequence reads.

ABSTRACT:

Background

Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challenging to do repeat analysis for species with highly repetitive or complex genomes which often do not have good reference genomes or annotated repeat libraries. Recently we developed a computational method called REPdenovo that constructs consensus repeat sequences directly from short sequence reads, which outperforms an existing tool called RepARK. One major issue with REPdenovo is that it doesn't perform well for repeats with relatively high divergence rates or low copy numbers. In this paper, we present an improved approach for constructing consensus repeats direc

SUBMITTER: Chu C 

PROVIDER: S-EPMC6101065 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature