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Awesome Ribo-Seq

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

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
RiboSeqDB Code Reference Appears to be defunct
TranslatomeDB Code Reference Transcriptome aligned with FANSe3; Link
svist4get Code Reference Command line app; Genomic

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
  • STATR (pipeline) Link

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

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

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

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
Code Reference

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
Code Reference

Unsorted list: