HARP: an automated platform for targeted resequencing data analysis

Abstract

Motivation and Objectives The fast-evolving scenario of Next Generation Sequencing (NGS) technologies caused an increasing demand of ready-to-use, costless and computationally powerful analysis systems, that could both represent a straightforward way to analyze huge amounts of data and offer a set of well assessed protocols to guide the user into an extensive landscape of different standards. In this session, I will present a simple tool called Hierarchical Assisted Resequencing Platform (HARP). HARP is an integrated NGS analysis platform, oriented especially towards resequencing experiments. HARP features allow the user to create personalized resequencing pipelines, using different tools and simplifying their usage and tuning; lead multiple projects at the same time; produce, manipulate, analyze and store data; a user-friendly interface, and finally create graphs, reports and benchmark protocols to assess the final results. Many general purpose platforms, such as Crossbow (Langmead et al. 2009), CloudBurst (Shatz 2009) or Galaxy (Goecks et al. 2010), have been successfully created, providing instruments for computationally intensive analyses directly on internet, without the need of huge hardware facilities. HARP has been prepared with the same purposes, but with the final goal of providing a risk evaluation parameter connected with the clinical and personal genetic profile of breast cancer affected patients.