Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data? Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?
Most of these use RNA-seq data, some use WGS data, and some use both. They are listed alphabetically. I will add to the list when I discover more.


Barnacle: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-550
Bellerophontes: http://bioinformatics.oxfordjournals.org/content/28/16/2114.long
BreakDancer: http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
BreakFusion: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389765/
BreakPointer: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561864/
ChimeraScan: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187648/
Comrad: http://bioinformatics.oxfordjournals.org/content/27/11/1481.long
CRAC: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053775/
deFuse: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001138
Dissect: http://bioinformatics.oxfordjournals.org/content/28/12/i179.abstract
EBARDenovo: http://bioinformatics.oxfordjournals.org/content/early/2013/03/01/bioinformatics.btt092
EricScript: http://bioinformatics.oxfordjournals.org/content/28/24/3232
FusionAnalyser: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439881/
FusionCatcher: http://biorxiv.org/content/early/2014/11/19/011650.full-text.pdf+html
FusionFinder: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384600/
FusionHunter: http://bioinformatics.oxfordjournals.org/content/27/12/1708.long
FusionMap: http://bioinformatics.oxfordjournals.org/content/27/14/1922
FusionQ: http://www.biomedcentral.com/1471-2105/14/193
FusionSeq: http://www.genomebiology.com/2010/11/10/R104
IDP-fusion: http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv562.full
iFUSE: http://bioinformatics.oxfordjournals.org/content/29/13/1700.long
InFusion: https://bitbucket.org/kokonech/infusion/wiki/Home
INTEGRATE: http://www.ncbi.nlm.nih.gov/pubmed/26556708
JAFFA: http://www.genomemedicine.com/content/7/1/43
LifeScope: http://www.thermofisher.com/no/en/home/life-science/sequencing/next-generation-sequencing/solid-next-generation-sequencing/solid-next-generation-sequencing-data-analysis-solutions/lifescope-data-analysis-solid-next-generation-sequencing/lifescope-genomic-analysis-software-solid-next-generation-sequencing.html
MapSplice: http://www.ncbi.nlm.nih.gov/pubmed/20802226
MOJO https://github.com/cband/MOJO
nFuse: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483554/
Pegasus: http://www.biomedcentral.com/1752-0509/8/97
PRADA: http://www.ncbi.nlm.nih.gov/pubmed/24695405
ShortFuse: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072550/
SnowShoes-FTD: http://nar.oxfordjournals.org/content/39/15/e100
SOAPFuse: http://www.genomebiology.com/2013/14/2/R12
SOAPFusion: http://www.ncbi.nlm.nih.gov/pubmed/24123671
STAR: http://bioinformatics.oxfordjournals.org/content/29/1/15
STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion/wiki
TopHat-Fusion: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612/
TRUP: http://www.genomebiology.com/2015/16/1/7
ViralFusionSeq: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582262/


Other useful programs:

Chimeraviz (visualization tools for gene fusions): https://www.ncbi.nlm.nih.gov/pubmed/28525538 (disclaimer: I created this)

Chimera: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253834/
OncoFuse: http://bioinformatics.oxfordjournals.org/content/29/20/2539.long
FuMa: http://bioinformatics.oxfordjournals.org/content/early/2015/12/09/bioinformatics.btv721.abstract