INIGO/Olivia: A Fast and Highly Accurate Tool for Detecting Mobile Element Insertions from High-Throughput Sequencing Data.

Son Pham, Han Do, Carol Marchetto, Inigo Narvaiza* and Fred Gage*

Transposable elements have been shaping the genome throughout evolution, contributing to the creation of new genes and rapidly changed the genomic architecture. The most common transposable element is ALU, a 300-bp element, with about 1 million copies in the human genome. Detecting ALU using the current short-read sequencing data is impeded by the large number of short reads, and the low mappability of these highly repetitive sequences. We have developed an algorithm, called INIGO, to detect non-reference ALU insertions using the current high throughput short read sequencing data from both whole genome (DNA-Seq) and whole transcriptome (RNA-Seq) studies. When the RNA-Seq data are available, INIGO further detects the effects of the new insertions to the expression and splicing of the affected genes. INIGO software is freely available under the GNU General Public License.