Tools

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Fusion Gene Study-Tools


Mapping tools

Bowtie
RSEM
TopHat
TheTuxedoSuite
Bowtie, Tophat, and Cufflinks

Assembly tools

Trinity
Oases
EBARDenovo

Chimera detection tools

Perl scripts

SAOPfuse
2013 Wu J
SAOPfusion
2013 Wu J
FusionFinder
2012 Francis RW
deFuse
2011 Andrew McPherson
FusionHunter
2011 Yang Li
SnowShoes-FTD
2011 YW Asmann
ViralFusionSeq
2013 JW Li

Python scripts

ChimeraScan
2009 MK Iyer
FusionCatcher
2014 D Nicorici
PRADA
2014

C/C++ programs

TopHat-Fusion
2011 D Kim
MapSplice
2010 K Wang
BreakDancer
2009 K Chen
FusionSeq
2010 A Sboner

C# programs

FusionMap
2011 H Ge
FusionAnalyser
2012 R Piazza

R package

chimera
2014 M Beccuti

Visualization tools

UGENE

Other NGS tools

samtools gmap

Iso images

FusionMint
Linux Mint 17.1 “Rebecca”
RNAMint
Linux Mint 17.1 “Rebecca”

Programming API

EMBL-EBI Web Services
http://www.ebi.ac.uk/Tools/webservices

Links

http://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools