Table 1.

Summery of computational tools for fusion transcripts detection.

Tools	Installation	URL	Reference
INTEGRATE	C++	https://sourceforge.net/projects/integrate-fusion/	[64]
FusionMatcher	Python script	https://github.com/ErasmusMC-Bioinformatics/fuma	[65]
IDP-fusion	Python script	http://www.healthcare.uiowa.edu/labs/au/IDP-fusion/	[40]
JAFFA	Java script	https://github.com/Oshlack/JAFFA/wiki	[42]
NCLscan	Python script	https://github.com/TreesLab/NCLscan	[66]
TRUP	Perl script	https://github.com/ruping/TRUP	[46]
ChildDecode	-	http://www.fusiongenomics.com/onetestproducts/	[67]
FusionCatcher	Python script	http://code.google.com/p/fusioncatcher/	[68]
Pegasus	Java, Perl and Python	http://sourceforge.net/projects/pegasus-fus/	[69]
PRADA	Python script	http://bioinformatics.mdanderson.org/main/PRADA:Overview	[70]
CRAC	C++ script	http://crac.gforge.inria.fr	[38]
FusionQ	Perl script	https://sites.google.com/site/fusionq1/home/	[47]
SOAPFuse	Perl script	http://soap.genomics.org.cn/soapfuse.html	[71]
SOAPfusion		http://soap.genomics.org.cn/SOAPfusion.html
Bellerophontes	Java script	http://eda.polito.it/bellerophontes/	[43]
BreakFusion	Several tools	http://bioinformatics.mdanderson.org/main/BreakFusion	[54]
elDorado	-	https://www.genomatix.de/index.html	[72]
Dissect	C++ script	http://dissect-trans.sourceforge.net/Home	[44]
EricScript	Perl and R	http://sourceforge.net/projects/ericscript/	[73]
FusionAnalyser	C#,Window/Linux based	http://www.ngsbicocca.org/html/fusion_analyser.html	[61]
FusionFinder	Perl script	http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/	[74]
LifeScope		https://www.thermofisher.com/uk/en/home/technical-resources/software-downloads/lifescope-genomic-analysis-software.html
nFuse	Perl script	https://code.google.com/p/nfuse/	[41]
ChimeraScan	C++ script	http://code.google.com/p/chimerascan/	[57]
Comrad	C++ and Perl	https://code.google.com/p/comrad/	[37]
deFuse	C++ script	http://sourceforge.net/projects/defuse/	[11]
FusionHunter	Perl script	http://bioen-compbio.bioen.illinois.edu/FusionHunter/	[60]
FusionMap	Executable file	http://www.arrayserver.com/wiki/index.php?title=FusionMap	[39]
ShortFuse	C++ script	https://bitbucket.org/mckinsel/shortfuse	[59]
SnowShoes-FTD	Perl Script	http://bioinformaticstools.mayo.edu/research/snowshoes-ftd/	[58]
TopHat-Fusion	Python script	http://tophat.cbcb.umd.edu/fusion_index.html	[35]
FusionSeq	C script	http://archive.gersteinlab.org/proj/rnaseq/fusionseq/	[29]
MapSplice	Python script	http://www.netlab.uky.edu/p/bioinfo/MapSplice	[45]