Galaxy RNA Workbench

Welcome to the RNA Galaxy workbench 2.0

The RNA Galaxy workbench is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.

The current implementation comprises more than 700 bioinformatics tools 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. Out of these 700 tools about 100 tools were integrated into galaxy by us and the remaining are from the galaxy community efforts.

The workbench is developed by the RNA Bioinformatics Center (RBC). This center is one of the eight service units of the German Network for Bioinformatics Infrastructure (de.NBI), running the German ELIXIR Node.

Cite

If you find this resource useful, please cite The RNA workbench 2.0: next generation RNA data analysis.

Get started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour through Galaxy’s user interface.

Training

We are passionate about training. So we are working in close collaboration with the Galaxy Training Network (GTN) to develop training materials of data analyses based on Galaxy (Batut et al. 2017). These materials hosted on the GTN GitHub repository are available online at https://training.galaxyproject.org.

Want to learn more about RNA analyses? Take one of our guided tour or check out the following hands-on tutorials. We developed several tutorials and the remaining are from the GTN community (marked with )

Lesson	Slides	Hands-on	Input dataset	Workflows	Galaxy tour	Galaxy History
Introduction to Transcriptomics
RNA-seq counts to genes
RNA-seq genes to pathways
RNA-Seq reads to counts
Analyse unaligned ncRNAs
CLIP-Seq data analysis from pre-processing to motif detection
De novo transcriptome reconstruction with RNA-Seq
Differential abundance testing of small RNAs
Network analysis with Heinz
PAR-CLIP analysis
Reference-based RNA-Seq data analysis
RNA family model construction
RNA-RNA interactome data analysis
RNA-seq counts to genes
RNA-seq genes to pathways
RNA-Seq reads to counts
Scan for C/D-box sequences with segmentation-fold
Small Non-coding RNA Clustering using BlockClust
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with heatmap2
ViennaRNA Introduction

Available tools

In this section we list all tools that have been integrated in the RNA workbench. The list is likely to grow as soon as further tools and workflows are contributed. To ease readability, we divided them into categories.

RNA structure prediction and analysis

Tool	Description	Reference
antaRNA	Possibility of inverse RNA structure folding and a specification of a GC value constraint	Kleinkauf et al. 2015
CoFold	A thermodynamics-based RNA secondary structure folding algorithm	Proctor and Meyer, 2015
Kinwalker	Algorithm for cotranscriptional folding of RNAs to obtain the min. free energy structure	Geis et al. 2008
MEA	Prediction of maximum expected accuracy RNA secondary structures	Amman et al. 2013
RNAshapes	Structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features	Janssen and Giergerich, 2014
RNAz	Predicts structurally conserved and therm. stable RNA secondary structures in mult. seq. alignments	Washietl et al. 2005
segmentation-fold	An application that predicts RNA 2D-structure with an extended version of the Zuker algorithm	-
ViennaRNA	A tool compilation for prediction and comparison of RNA secondary structures	Lorenz et al. 2011

RNA alignment

Tool	Description	Reference
Compalignp	An RNA counterpart of the protein specific “Benchmark Alignment Database”	Wilm et al. 2006
LocARNA	A tool for multiple alignment of RNA molecules	Will et al. 2012
MAFFT	A multiple sequence alignment program for unix-like operating systems	Katoh and Standley, 2016
RNAlien	A tool for RNA family model construction	Eggenhofer et al. 2016
CMV	RNA family model visualisation	Eggenhofer et al. 2018

RNA annotation

Tool	Description	Reference
ARAGORN	A tool to identify tRNA and tmRNA genes	Laslett and Canback, 2004
Fusion Matcher (FuMa)	A tool that reports identical fusion genes based on gene-name annotations	Hoogstrate et al. 2016
GotohScan	A search tool that finds shorter sequences in large database sequences	Hertel et al. 2009
INFERNAL	A tool searching DNA sequence databases for RNA structure and sequence similarities	Nawrocki et al. 2015
RNABOB	A tool for fast pattern searching for RNA secondary structures	-
RNAcode	Predicts protein coding regions in a a set of homologous nucleotide sequences	Washietl et al. 2011
tRNAscan	Searches for tRNA genes in genomic sequences	Lowe and Eddy, 1997
RCAS	A generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments	Uyar et al.

RNA-protein interaction

Tool	Description	Reference
AREsite2	A database for AU-/GU-/U-rich elements in human and model organisms	Fallmann et al. 2016
DoRiNA	A database of RNA interactions in post-transcriptional regulation	Blin et al. 2014
PARalyzer	An algorithm to generate a map of interacting RNA-binding proteins and their targets	Corcoran et al. 2011
Piranha	A peak-caller for CLIP- and RIP-seq data	-

RNA-RNA interaction

Tool	Description	Reference
C h i R A	A set of tools to analyze RNA interactome/structurome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH etc	-

RNA target prediction

Tool	Description	Reference
TargetFinder	A tool to predict small RNA binding sites on target transcripts from a sequence database	-

RNA Seq and HTS analysis

Preprocessing

Tool	Description	Reference
FastQC	A quality control tool for high throughput sequence data	-
Trim Galore!	Automatic quality and adapter trimming as well as quality control	-

RNA-Seq

Tool	Description	Reference
BlockClust	Small non-coding RNA clustering from deep sequencing read profiles	Videm et al. 2014
FlaiMapper	A tool for computational annotation of small ncRNA-derived fragments using RNA-seq data	Hoogstrate et al. 2015
MiRDeep2	Discovers microRNA genes by analyzing sequenced RNAs	Friedländer et al. 2008
NASTIseq	A method that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries	Li et al. 2013
PIPmiR	An algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features	Breakfield et al. 2011
SortMeRNA	A tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and -genomic data	Kopylova et al. 2011

Read Mapping

Tool	Description	Reference
hisat2	Hierarchical indexing for spliced alignment of transcripts	Pertea et al. 2016
RNA STAR	Rapid spliced aligner for RNA-seq data	Dobin et al. 2013
STAR-fusion	Fast fusion gene finder	Haas et al. 2017
bowtie2	Fast and sensitive read alignment	Langmead et al. 2012
BWA	Software package for mapping low-divergent sequences against a large reference genome	Li and Durbin 2009, Li and Durbin 2010

Transcript Assembly

Tool	Description	Reference
Trinity	De novo transcript sequence reconstruction from RNA-Seq	Haas et al. 2013

Quantification

Tool	Description	Reference
featureCounts	Ultrafast and accurate read summarization program	Liao et al. 2014
htseq-count	Tool for counting reads in features	Anders et al. 2015
Sailfish	Rapid Alignment-free Quantification of Isoform Abundance	Patro et al. 2014
Salmon	Fast, accurate and bias-aware transcript quantification	Patro et al. 2017

Differential expression analysis

Tool	Description	Reference
DESeq2	Differential gene expression analysis based on the negative binomial distribution	Love et al. 2014

Utilities

Tool	Description	Reference
SAMtools	Utilities for manipulating alignments in the SAM format	Heng et al. 2009
BEDTools	Utilities for genome arithmetic	Quinlan and Hall 2010
deepTools	Tools for exploring deep-sequencing data	Ramirez et al. 2014, Ramirez et al. 2016

Ribosome profiling

Tool	Description	Reference
RiboTaper	An analysis pipeline for Ribo-Seq experiments, exploiting the triplet periodicity of ribosomal footprints to call translated regions	Calviello et al. 2016

Contributors

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