deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramírez(Max Planck Institute of Immunobiology and Epigenetics), Devon Ryan(Max Planck Institute of Immunobiology and Epigenetics), Björn Grüning(University of Freiburg), Vivek Bhardwaj(University of Freiburg), Fabian Kilpert(Max Planck Institute of Immunobiology and Epigenetics), Andreas S. Richter(Max Planck Institute of Immunobiology and Epigenetics), Steffen Heyne(Max Planck Institute of Immunobiology and Epigenetics), Friederike Dündar(Cornell University), Thomas Manke(Max Planck Institute of Immunobiology and Epigenetics)
Nucleic Acids Research
April 13, 2016
10.1093/nar/gkw257
Cited by 8,951Open Access
Full Text

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.

Related Papers

No related papers found

Powered by citation graph analysis