Our paper entitled “An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data” has been accepted by Pacific Symposium on Biocomputing (PSB) 2018, and the proceeding of the paper is out now!
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.
However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data. We benchmarked our tool against TEtranscripts, a widely used TE quantification method, and three other quantification methods using several RNA-seq datasets from Drosophila melanogaster and human cell-line. We achieved 20 times faster execution speed without compromising the accuracy. This pipeline will enable the biomedical research community to quantify and analyze TEs from large amounts of data and lead to novel TE centric discoveries.
- Link to the paper: http://www.worldscientific.com/doi/pdf/10.1142/9789813235533_0016
- Link to PSB 2018 proceeding: http://www.worldscientific.com/worldscibooks/10.1142/10864
- Link to SalmonTE: https://github.com/hyunhwaj/SalmonTE