Awesome Ribo-Seq

A list of bioinformatic tools for working with Ribo-Seq data. Please feel free to make updates (a work in progress)

Table of Contents

Table of Contents

• Data Resources and Visualisation Environments
• Data Processing and Analysis
• Differential Analysis
• Quality Control
• Offset Determination
• ORF Calling
• ORF Databases
• Isoform Level Analysis
• Ribo-Seq Simulation
• Occupancy Analysis
• Pause Prediction
• Frameshift Detection
• Misc

Data Resources and Visualisation Environments

Tool	Code	Reference	Note(s)
Trips-Viz	Code	Reference	Written in Python; Browser only; Link; Transcriptome
GWIPS-viz	Code	Reference	Based on UCSC Genome Browser; Browser only; Link; Genome
RiboCrypt	Code	Reference	Written in R; Available in Bioc; Genome aligned; Visualisation in both
RPFdb	Code	Reference	Browser only; Counts and Called ORFs (RibORF) available per study; Genome; Link
HRPDviewer	Code	Reference	Pipeline available in .zip only' Written in Python; Transcriptome
HRPDviewer	Code	Reference	Pipeline available in .zip only' Written in Python; Transcriptome
RiboSeqDB	Code	Reference	Appears to be defunct
TranslatomeDB	Code	Reference	Transcriptome aligned with FANSe3; Link
svist4get	Code	Reference	Command line app; Genomic
RiboPlot	Code	Reference	Python; Archived
RiboPlotR	Code	Reference	R; Similar transcript plotting to RiboCrypt (w/ multiple isoforms)
RiboGraph	Code	Reference	Docker image; Endpoint for RiboPy

Data Processing and Analysis

Tool	Code	Reference	Note(s)
riboviz	Code	Reference	Nextflow (DSL1); End-to-end processing and analysis
Shoelaces	Code	Reference	Written in python
ORFik	Code	Reference	Written in R; Available on Bioc; End-to-end
RiboProfiling	Code	Reference	Written in R; Available on Bioc; Analysis Package
SystemPipeR	Code	Reference	Written in R; Available on Bioc; End-to-end
RiboStreamR	Code	Reference	Written in R; Available as web app
RiboSeqR	Code	None	Written in R; Available in Bioc; Analysis and visualisation
RiboPip	Code	None	Written in Ruby; Comes with Dockfile; End-to-end
RiboGalaxy	Code	Reference	Galaxy Platform; Tools in toolshed; Data Processing; Link
Plastid	Code	Reference	Written in Python; Packaged on PyPi; Analysis
RiboTools	Code	Reference	Galaxy Platform; Tools in toolshed; Analysis
RiboFlow, RiboR and RiboPy	Code	Reference	Ecosystem of tools; Nextflow (DSL1), R and Python; End-to-end
RiboToolKit	Code	Reference	Browser only; End-to-end; Link
XPRESSpipe	Code	Reference	Written in Python, R & C++; End-to-end
Ohler-Lab Pipeline	Code	None	Not a published pipeline; R; Shell; ORFquant; RiboseQC
Bushell-Lab Pipeline	Code	None	Not a published pipeline; R; Shell; End-to-end
Saket Choudhary Pipeline	Code	None	Not a published pipeline; Snakemake; STAR; RSEM
Firth Lab Ribo-Seq Manual	Code	None	Not a published pipeline; Tutorial; Shell
USA FDA Ribo-Seq Pipeline	Code	None	Not a published pipeline; Python; HISAT
scRibo-Seq paper	Code	Reference	Publication Code; Nextflow; R for figures
STATR	Code	Reference	Bacterial Ribo-Seq pipeline; Shell; Python; R
Ribomake	Code	Reference	Ribo-Seq Data Processing; Snakemake; Paired with RiboSeeker
RiboSeeker	Code	Reference	Downstream Analysis; R; Paired with Ribomake
Riboconsensus	Code	Reference	Python; Translation Heterogeneity
RiboDoc	Code	Reference	Docker; R; Image for end-to-end ribo-seq analysis
RiboLog	Code	Reference	R; Regression based tools for Ribo-Seq analysis Heterogeneity
RiboFootprintR	Code	Reference	R; Pipeline for data processing
RibofootPrinter	Code	Reference	Python; Toolbox for data analysis;
MassiveNGSPipe	Code	Reference	R; Fully automated end to end data processing; RiboCrypt data processing
mRibo	Code	Reference	Python; meta-gene analysis on microbial (Bacteria and Archaea) data

Differential Analysis

Tool	Code	Reference	Note(s)
Anota2Seq	Code	Reference	Written in R; Avaialble in Bioc
Babel	Code	Reference	Written in R; Available in CRAN; EdgeR
RiboDiff	Code	Reference	Python2, Galaxy, Link, GLM
Riborex	Code	Reference	Written in R; Conda installation; DEseq2, EdgeR, Voom;
RIVET	Code	Reference	Written in R; R Shiny app; Link defunct; EdgeR/Limma
Xtail	Code	Reference	Written in R; Available in DockerHub; Probability Distribution based
RiboDiPa	Code	Reference	Written in R; Available in Bioc; Differential analysis of binned p-seq counts
DeltaTE	Code	Reference	Written in R; Differential analysis; DESeq2

Quality Control

Tool	Code	Reference	Note(s)
MQc	Code	Reference	Written in Perl, Python 2, R; Available on Galaxy and Conda
Ribo-seQC	Code	Reference	Written in R
RiboQC	Code	Reference	Written in R; Part of RiboVIEW
ribosomeProfilingQC	Code	Reference	Written in R; Available on Bioc; Reference in Bioc link
ORFikQC	Code	Reference	Written in R; Available on Bioc; Part of ORFik
RiboScore	Code	None	Written in Python;

Note: Many more tools carry out QC as part of their functionality. Above are those that have individual QC specific modules (that I have seen so far).

Offset Determination

Tool	Code	Reference	Note(s)
Ribodeblur	Code	Reference	Written in Python
RiboProP	Code	Reference	Written in Julia; MNase Offset detection
RiboWaltz	Code	Reference	Written in R; Available in Bioconda
Integer Programming	Code	Reference	Written in Python; Paper contains comparison of methods
Scikit-ribo	Code	Reference	Written in Python; Also estiamtes translation efficiency
RiboA	Code	Reference	Written in Python; Django app in docker image; GUI for Integer Programming method above

Note: Many many tools carry out offset determinations. These ones advertise it as a main feature.

ORF Calling

Tool	Code	Reference	Note(s)
DeepRibo	Code	Reference	Python3/PyTorch; Prokaryotes; Ribo-Seq + SD sequence
RiboTricer	Code	Reference	Python; 3' periodicity based
orfRater	Code	Reference	Python, Regression based
PreTis	None Found	Reference	No code available; Webservice; Regression based TIS
PRICE	Code	Reference	Available as part of Gedi; Probablistic inference by EM
Proteoformer	Code	Reference	ORF calling for MS validation; Python, Perl
REPARATION	Code	Reference	Reannoation of Bacterial Genomes; Perl
RiboCode	Code	Reference	Wilcoxon Signed rank test of 3 frames; Python; On Bioconda
riboHMM	Code	Reference	Python2; Limits to 1 coding sequence per transcript
RibORF	Code	Reference	Perl; 3' periodicity, uniformness;
Ribosome profiling analysis framework	Code	Reference	PHP, Organism must be on Mutalyzer
RiboTaper	Code	Reference	R; Multitaper analysis of triplet; Bioconda, Galaxy;
Ribo-TISH	Code	Reference	Python; TI-seq (TIS Hunter); Supports differential initiation analysis
RiboWave	Code	Reference	R, Perl, Shell; Wavelet Transform;
Rp-Bp	Code	Reference	Python; End-to-end pipeline; Bayesian Periodic fragment length and ribosome P-site offset Selection
SPECtre	Code	Reference	Python; Spectral analysis of sliding windows
uORF-seqr	Code	Reference	R; ML-approach; Methods unclear as paper describes regression
uORF4u	Code	Reference	Python; Not Ribo-Seq; Conservation based; One 5' UTR at a time
ORFLine	Code	Reference	Shell, R, Perl, Python; End-to-end; Plastid + ORFscore
RiboNT	Code	Reference	Python; Noise tolerence
Ribofy	Code	None Found	Python; Statistical enrichment on inframe P-sites
HRIBO	Code	Reference	Snakemake; Bacterial ORF Detection; DeepRibo; REPARATION
uORF_Annotator	Code	Reference	Python; Manually annotated training set; ORF and TIS prediction (according to paper)
iRibo	Code	Reference	C++; Binomial test for three nucleotide; Empirical false discovery rate; Aggregated data periodicity
ORFScore	Code	Reference	# in-frame reads; Comparison to uniform dist
AltORFev	Code	Reference	No Code & web app broken - scanning based mechanism of ORF prediction

ORF Databases

Tool	Link	Reference	Note(s)
sORFs.org	Link	Reference	ORFs Detected with Proteoformer; Pride reprocessing
OpenProt	Link	Reference	Ribo-Seq + Mass Spec; Polycistronic gene models
smProt	Link	Reference	Small protein database rather than ORFs
nORFs.org	Link	Reference	Aggregated database of OpenProt and sORFs.org; Nice UI
uORF-db	Link	Reference	"Literature, sequence, and variation data in a central hub"
	Link	Reference

Isoform Level Analysis

Tool	Code	Reference	Note(s)
Ribomap	Code	Reference	C++; Salmon; Isoform level ribosome profiles based on transcript abundance
ORFquant	Code	Reference	R; Isoform level translation quantification of ORFs
ORQAS	Code	Reference	Python, Shell; Isoform level quantification extending Ribomap
RPiso	Code	Reference	Perl; RSEM: Isoform level analysis
RiboZINB	Code	None Found	Perl, R; Identifying actively translated isoform
DeepShape	Code	Reference	Python; RNA-Seq free Isoform level quantification
RiboCalc	Code	Reference	R; quantitatively modeling of coding ability
RiboMIMO	Code	Reference	Python; Multi-Input Multi-Output full isoform density prediction
	Code	Reference

Ribo-Seq Simulation

Tool	Code	Reference	Note(s)
RiboSimR	Code	Reference	R; Simulation and Power analysis; Available
coverageSim	Code	Reference	R; Comprehensive simulation of full profiles
simRiboSeq	Code	Reference	R; Footprint simulator; Unclear differences with coverageSim
Ribo-Seq Modelling	Code	Reference	R; Footprint simulator; Unclear differences with coverageSim

Occupancy Analysis

Tool	Code	Reference	Note(s)
RUST	Code	Reference	Python; Unit step transform; Meta analysis
Ribo-DT	Code	Reference	Snakemake; generalized linear model (GLM)
Concur	Code	Reference	Perl; R; Codon counts from Ribo-seq
Diricore	"Available On Request"	Reference

Pause Prediction

Tool	Code	Reference	Note(s)
PausePred	Code	Reference	Perl; Sliding Window
ROSE	Code	Reference	Python; Scikit-learn

Frameshift Detection

Tool	Code	Reference	Note(s)
ORFeus	Code	Reference	Python; HMM; detects many different alt-ORF types

Misc

Tool	Code	Reference	Note(s)
RFoot	Code	Reference	Perl; Finding RNA-Protein complexes from Ribo-Seq
choros	Code	Reference	R; Estimate and Correct Sequence Bias in Ribo-Seq
RiboReport	Code	Reference	Snakemake; Bacterial ORF detection Benchmarking
RiboShape	Code	Reference	Generation of Ribosome Profiles from sequence; MATLAB
RiboShape (different)	Code	Reference	Workflow for analysis of RNA structure impact on translation
RiboFormer	Code	Reference	Python; Transformer for Ribo-Seq Profile Prediction
Translatomer	Not Published Yet	Reference	Python; multimodal transformer; predicts cell-type-specific profiles
RiboGL	Code	Reference	Python; Ribosome Density prediction with GCN and BiLSTM

Unsorted list:

• RCSU RS (https://doi.org/10.1093/dnares/dsw062)

• RiboStan (Ohler Lab) Link