title: deepTools: a flexible platform for exploring deep-sequencing data.
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.
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors.forename: Fidel
authors.initials: F
authors.lastname: Ramírez
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany.
authors.forename: Friederike
authors.initials: F
authors.lastname: Dündar
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Diehl
authors.affiliation: Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
authors.forename: Björn A
authors.initials: BA
authors.lastname: Grüning
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany manke@ie-freiburg.mpg.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Manke
mesh_terms: D003196:Computer Graphics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D020407:Internet; D012984:Software