JAFFA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool JAFFA

Tool usage distribution map

This map represents all the scientific publications referring to JAFFA per scientific context
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Associated diseases


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JAFFA specifications


Unique identifier OMICS_08416
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Raw RNA-Seq reads or pre-assembled transcripts
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Nadia Davidson

Publication for JAFFA

JAFFA citations


Gaining comprehensive biological insight into the transcriptome by performing a broad spectrum RNA seq analysis

Nat Commun
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] s and development of various cancer types. RNA-seq has been shown as a valuable source for detecting fusion genes. Several tools have been proposed to identify fusion from transcriptomic data such as JAFFA, STAR-Fusion, TopHat-Fusion, FusionCatcher, and SOAPfuse. In addition to these short-read-based techniques, IDP-fusion, and Iso-Seq methods can analyse long-read RNA-seq data to identify fused g […]


chimeraviz: a tool for visualizing chimeric RNA

PMCID: 5870674
PMID: 28525538
DOI: 10.1093/bioinformatics/btx329

[…] Using chimeraviz, the user can import data from nine fusion-finders: deFuse (), EricScript (), InFusion (), JAFFA (), FusionCatcher (), FusionMap (), PRADA (), SOAPfuse () and STAR-FUSION (). With transcript annotation data from Ensembl and aligned RNA-sequencing data in a .BAM file, the user can create mul […]


Discovering and understanding oncogenic gene fusions through data intensive computational approaches

Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] BreakDancer () and CREST (), can call gene fusions in addition to other structural rearrangements. In the last 2 years, several additional fusion mapping tools have been released—FusionMetaCaller (), JAFFA (), IDP-fusion (), TRUP (), FusionCatcher and PRADA (). A number of supporting tools, such as the Bioconductor package Chimera (), offer utilities for organizing, analyzing and validating gene f […]


Comparative assessment of methods for the fusion transcripts detection from RNA Seq data

Sci Rep
PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] Bellerophontes, BreakFusion, Chimerascan, nFuse, EricScript, FusionCatcher, FusionHunter, FusionMap, JAFFA, MapSplice, SOAPfuse, and TopHat-Fusion packages were downloaded and installed on our server (http://uvacse.virginia.edu/resources/rivanna/rivanna). All of the software packages were run using a […]


Landscape of gene fusions in epithelial cancers: seq and ye shall find

Genome Med
PMCID: 4683719
PMID: 26684754
DOI: 10.1186/s13073-015-0252-1

[…] atics pipelines have been developed to help prioritize fusion candidates from next-generation sequencing (NGS) data, including Chimerascan [], FusionSeq [], DeFuse [], TopHat-Fusion [], PRADA [], and JAFFA []. While useful to help reduce the number of false candidates, the output from bioinformatics pipelines needs to be further validated, preferably followed by functional assays, before designati […]

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JAFFA institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Victoria, Australia

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