JAFFA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool JAFFA
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Tool usage distribution map

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

Information


Unique identifier OMICS_08416
Name JAFFA
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

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Documentation


Maintainer


  • person_outline Nadia Davidson

Publication for JAFFA

JAFFA citations

 (5)
library_books

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

2017
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 […]

library_books

chimeraviz: a tool for visualizing chimeric RNA

2017
Bioinformatics
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 […]

library_books

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

2016
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 […]

library_books

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

2016
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 […]

library_books

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

2015
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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