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Welcome to the RNA Galaxy workbench 2.0

RNA Galaxy

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.

Content

  1. Get started
  2. Training
  3. Available tools
    1. RNA structure prediction and analysis
    2. RNA alignment
    3. RNA annotation
    4. RNA-protein interaction
    5. RNA-RNA interaction
    6. RNA target prediction
    7. RNA Seq and HTS analysis
    8. Ribosome profiling
  4. Contributors

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
ChiRA 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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