JAFFA statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Gene fusion detection chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

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



Add your version



  • person_outline Nadia Davidson <>

Publication for JAFFA

JAFFA in publications

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

[…] 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 […]

PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] () 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 […]

PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] tools (i.e. fusionhunter, fusionmap, fusionfinder, mapsplice, defuse, and tophat-fusion) with positive and negative datasets. however, several newly developed tools like breakfusion, soapfuse, jaffa, nfuse, ericscript, and fusioncatcher were not included in this study. even though some comparisons were included in the papers from the developers of these new software tools, […]

To access a full list of publications, you will need to upgrade to our premium service.

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

JAFFA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review JAFFA