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Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Author information

1
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, D-79110 Freiburg, Germany.
2
Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany.
3
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
4
Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13125, Berlin, Germany.
5
Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.
6
Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstr. 69, D-18051 Rostock, Germany.
7
Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.
8
Department of Urology, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands.
9
Departments of Biology and Computer Science, Humboldt University, Unter den Linden 6, D-10099 Berlin.
10
Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany.
11
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.
12
BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schänzlestr. 18, D-79104 Freiburg, Germany.

Abstract

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis.

AVAILABILITY:

The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench.

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