text: user283: Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?
  
  user283: 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
  
original_text: 283: <p>Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?</p>
   283: <p>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.</p>
  
  <ol>
  <li>Barnacle: <a href="http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-550" rel="noreferrer">http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-550</a></li>
  <li>Bellerophontes: <a href="http://bioinformatics.oxfordjournals.org/content/28/16/2114.long" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/28/16/2114.long</a></li>
  <li>BreakDancer: <a href="http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html" rel="noreferrer">http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html</a></li>
  <li>BreakFusion: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389765/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389765/</a></li>
  <li>BreakPointer: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561864/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561864/</a></li>
  <li>ChimeraScan: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187648/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187648/</a></li>
  <li>Comrad: <a href="http://bioinformatics.oxfordjournals.org/content/27/11/1481.long" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/27/11/1481.long</a></li>
  <li>CRAC: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053775/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053775/</a></li>
  <li>deFuse: <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001138" rel="noreferrer">http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001138</a></li>
  <li>Dissect: <a href="http://bioinformatics.oxfordjournals.org/content/28/12/i179.abstract" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/28/12/i179.abstract</a></li>
  <li>EBARDenovo: <a href="http://bioinformatics.oxfordjournals.org/content/early/2013/03/01/bioinformatics.btt092" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/early/2013/03/01/bioinformatics.btt092</a></li>
  <li>EricScript: <a href="http://bioinformatics.oxfordjournals.org/content/28/24/3232" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/28/24/3232</a></li>
  <li>FusionAnalyser: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439881/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439881/</a></li>
  <li>FusionCatcher: <a href="http://biorxiv.org/content/early/2014/11/19/011650.full-text.pdf+html" rel="noreferrer">http://biorxiv.org/content/early/2014/11/19/011650.full-text.pdf+html</a></li>
  <li>FusionFinder: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384600/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384600/</a></li>
  <li>FusionHunter: <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1708.long" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/27/12/1708.long</a></li>
  <li>FusionMap: <a href="http://bioinformatics.oxfordjournals.org/content/27/14/1922" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/27/14/1922</a></li>
  <li>FusionQ: <a href="http://www.biomedcentral.com/1471-2105/14/193" rel="noreferrer">http://www.biomedcentral.com/1471-2105/14/193</a></li>
  <li>FusionSeq: <a href="http://www.genomebiology.com/2010/11/10/R104" rel="noreferrer">http://www.genomebiology.com/2010/11/10/R104</a></li>
  <li>IDP-fusion: <a href="http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv562.full" rel="noreferrer">http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv562.full</a></li>
  <li>iFUSE: <a href="http://bioinformatics.oxfordjournals.org/content/29/13/1700.long" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/29/13/1700.long</a></li>
  <li>InFusion: <a href="https://bitbucket.org/kokonech/infusion/wiki/Home" rel="noreferrer">https://bitbucket.org/kokonech/infusion/wiki/Home</a></li>
  <li>INTEGRATE: <a href="http://www.ncbi.nlm.nih.gov/pubmed/26556708" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pubmed/26556708</a></li>
  <li>JAFFA: <a href="http://www.genomemedicine.com/content/7/1/43" rel="noreferrer">http://www.genomemedicine.com/content/7/1/43</a></li>
  <li>LifeScope: <a href="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" rel="noreferrer">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</a></li>
  <li>MapSplice: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20802226" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pubmed/20802226</a></li>
  <li>MOJO <a href="https://github.com/cband/MOJO" rel="noreferrer">https://github.com/cband/MOJO</a></li>
  <li>nFuse: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483554/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483554/</a></li>
  <li>Pegasus: <a href="http://www.biomedcentral.com/1752-0509/8/97" rel="noreferrer">http://www.biomedcentral.com/1752-0509/8/97</a></li>
  <li>PRADA: <a href="http://www.ncbi.nlm.nih.gov/pubmed/24695405" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pubmed/24695405</a></li>
  <li>ShortFuse: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072550/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072550/</a></li>
  <li>SnowShoes-FTD: <a href="http://nar.oxfordjournals.org/content/39/15/e100" rel="noreferrer">http://nar.oxfordjournals.org/content/39/15/e100</a></li>
  <li>SOAPFuse: <a href="http://www.genomebiology.com/2013/14/2/R12" rel="noreferrer">http://www.genomebiology.com/2013/14/2/R12</a></li>
  <li>SOAPFusion: <a href="http://www.ncbi.nlm.nih.gov/pubmed/24123671" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pubmed/24123671</a></li>
  <li>STAR: <a href="http://bioinformatics.oxfordjournals.org/content/29/1/15" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/29/1/15</a></li>
  <li>STAR-Fusion: <a href="https://github.com/STAR-Fusion/STAR-Fusion/wiki" rel="noreferrer">https://github.com/STAR-Fusion/STAR-Fusion/wiki</a></li>
  <li>TopHat-Fusion: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612/</a></li>
  <li>TRUP: <a href="http://www.genomebiology.com/2015/16/1/7" rel="noreferrer">http://www.genomebiology.com/2015/16/1/7</a></li>
  <li>ViralFusionSeq: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582262/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582262/</a></li>
  </ol>
  
  <p><strong>Other useful programs:</strong></p>
  
  <p>Chimeraviz (visualization tools for gene fusions): <a href="https://www.ncbi.nlm.nih.gov/pubmed/28525538" rel="noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/28525538</a> (disclaimer: I created this)</p>
  
  <p>Chimera: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253834/" rel="noreferrer">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253834/</a><br>
  OncoFuse: <a href="http://bioinformatics.oxfordjournals.org/content/29/20/2539.long" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/29/20/2539.long</a><br>
  FuMa: <a href="http://bioinformatics.oxfordjournals.org/content/early/2015/12/09/bioinformatics.btv721.abstract" rel="noreferrer">http://bioinformatics.oxfordjournals.org/content/early/2015/12/09/bioinformatics.btv721.abstract</a></p>
  