title: deepTools2: a next generation web server for deep-sequencing data analysis.
abstract: We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
authors.forename: Fidel
authors.initials: F
authors.lastname: Ramírez
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
authors.forename: Devon P
authors.initials: DP
authors.lastname: Ryan
authors.affiliation: University of Freiburg, Department of Computer Science, 79110 Freiburg, Germany.
authors.forename: Björn
authors.identifier: 0000-0002-3079-6586
authors.initials: B
authors.lastname: Grüning
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
authors.forename: Vivek
authors.initials: V
authors.lastname: Bhardwaj
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Kilpert
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
authors.forename: Andreas S
authors.identifier: 0000-0002-4166-0991
authors.initials: AS
authors.lastname: Richter
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Heyne
authors.affiliation: Weill Cornell Medical College, Applied Bioinformatics Core, Department of Physiology and Biophysics, New York, NY 10065, USA.
authors.forename: Friederike
authors.initials: F
authors.lastname: Dündar
authors.affiliation: Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany manke@ie-freiburg.mpg.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Manke
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003196:Computer Graphics; D004331:Drosophila melanogaster / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*; D012984:Software