Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution.

ABSTRACT:

Background

Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases.

Results

Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping and clipped-read signatures produced by NGS alignments. Jitterbug can be easily integrated into existing NGS analysis pipelines, using the standard BAM format produced by frequently applied alignment tools (e.g. bwa, bowtie2), with no need to realign reads to a set of consensus transposo

SUBMITTER: Henaff E 

PROVIDER: S-EPMC4603299 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature