deepTools: a flexible platform for exploring deep-sequencing data

TLDR

We present a Galaxy‑based web server for processing and visualizing deeply sequenced data. The server’s core functionality is a suite of newly developed tools, deepTools, that let users with little bioinformatics background upload pre‑processed files in standard formats to generate customizable heatmaps, summary plots, and normalized coverage files, all within a modular, open‑source framework that can be expanded. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de, offers extensive documentation and tutorials, can be used without registration, and can also be installed locally as a stand‑alone or Galaxy component.

Abstract

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy.