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

TLDR

Since its 2014 launch, the deepTools Galaxy server has evolved to address community requests with new solutions. The authors update the Galaxy‑based web server to enhance processing, visualization, and interpretation of deeply sequenced data. deepTools2 extends the core deepTools suite with Galaxy workflows, command‑line tools, and a public API, enabling quality control, normalization, clustering, and visualization of aligned reads. The updated deepTools2 service remains freely available to all users at deeptools.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.