NGS ROI

Novel Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments

M. Holtgrewe, J.-Y. Coppee, K. Reinert, B. Jagla: Novel Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments, submitted.

Abstract

The analysis and interpretation of aligned data from high throughput sequencing experiments is mostly limited to visual inspection using a genome browser and specialized programs. Hence, it would be very beneficial if the inspection and interpretation of the data could be guided by more automated methods. We present here a framework for post alignment data analysis and show how this can be useful for quality control and in biological interpretation.

Downloads and Installation Instructions

We provide a binary package (for Linux systems) and the source code.

After downloading the binary archive, you will find the programs and scripts in the subfolder "bin". The README file contains detailed instructions and examples for getting started. In the near future we plan to provide binary downloads for Mac Os X, too. The folder share/R contains the ngsroi R package in both the Windows and Linux/Mac version.

The sources can be built as a SeqAn application (see the SeqAn Documentation for details).

You can find the Galaxy integration on the Galaxy Test Tool Shed.

Last Update 9. July 2013