Format

Send to

Choose Destination
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13.

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

Author information

1
Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
2
University of Freiburg, Department of Computer Science, 79110 Freiburg, Germany.
3
Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
4
Weill Cornell Medical College, Applied Bioinformatics Core, Department of Physiology and Biophysics, New York, NY 10065, USA.
5
Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany manke@ie-freiburg.mpg.de.

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.

PMID:
27079975
PMCID:
PMC4987876
DOI:
10.1093/nar/gkw257
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center