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Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?

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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.

  1. Barnacle: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-550
  2. Bellerophontes: http://bioinformatics.oxfordjournals.org/content/28/16/2114.long
  3. BreakDancer: http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
  4. BreakFusion: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389765/
  5. BreakPointer: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561864/
  6. ChimeraScan: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187648/
  7. Comrad: http://bioinformatics.oxfordjournals.org/content/27/11/1481.long
  8. CRAC: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053775/
  9. deFuse: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001138
  10. Dissect: http://bioinformatics.oxfordjournals.org/content/28/12/i179.abstract
  11. EBARDenovo: http://bioinformatics.oxfordjournals.org/content/early/2013/03/01/bioinformatics.btt092
  12. EricScript: http://bioinformatics.oxfordjournals.org/content/28/24/3232
  13. FusionAnalyser: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439881/
  14. FusionCatcher: http://biorxiv.org/content/early/2014/11/19/011650.full-text.pdf+html
  15. FusionFinder: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384600/
  16. FusionHunter: http://bioinformatics.oxfordjournals.org/content/27/12/1708.long
  17. FusionMap: http://bioinformatics.oxfordjournals.org/content/27/14/1922
  18. FusionQ: http://www.biomedcentral.com/1471-2105/14/193
  19. FusionSeq: http://www.genomebiology.com/2010/11/10/R104
  20. IDP-fusion: http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv562.full
  21. iFUSE: http://bioinformatics.oxfordjournals.org/content/29/13/1700.long
  22. InFusion: https://bitbucket.org/kokonech/infusion/wiki/Home
  23. INTEGRATE: http://www.ncbi.nlm.nih.gov/pubmed/26556708
  24. JAFFA: http://www.genomemedicine.com/content/7/1/43
  25. 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
  26. MapSplice: http://www.ncbi.nlm.nih.gov/pubmed/20802226
  27. MOJO https://github.com/cband/MOJO
  28. nFuse: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483554/
  29. Pegasus: http://www.biomedcentral.com/1752-0509/8/97
  30. PRADA: http://www.ncbi.nlm.nih.gov/pubmed/24695405
  31. ShortFuse: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072550/
  32. SnowShoes-FTD: http://nar.oxfordjournals.org/content/39/15/e100
  33. SOAPFuse: http://www.genomebiology.com/2013/14/2/R12
  34. SOAPFusion: http://www.ncbi.nlm.nih.gov/pubmed/24123671
  35. STAR: http://bioinformatics.oxfordjournals.org/content/29/1/15
  36. STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion/wiki
  37. TopHat-Fusion: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612/
  38. TRUP: http://www.genomebiology.com/2015/16/1/7
  39. 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

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1- Chimerascan + Star

2- Tophat Fusion

Two pipelines I have used extensively and recommend. The others listed by @L42 I can't speak to but Star Fusion sounds promising. Star is fast.

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