RetroSeq: transposable element discovery from next-generation sequencing data.

ABSTRACT: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.

Availabilty

RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.

SUBMITTER: Keane TM 

PROVIDER: S-EPMC3562067 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature