<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>

CC BY-SA 3.0
2017-05-31T10:05:01.120Z
2017-05-31T10:05:01.120Z
stianlagstad
<p>1- Chimerascan + Star</p>

<p>2- Tophat Fusion</p>

<p>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. </p>

CC BY-SA 3.0
2017-05-31T16:58:30.973Z
2017-05-31T16:58:30.973Z
111
<p>Given WGS data or RNA-seq data, which tools can I use to detect gene fusions?</p>

<rna-seq><wgs>
Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data?
# Which tools can detect chimeric RNA (fusion genes) from WGS or RNA-Seq data?

(Asked by: username_0 on 2017-05-31)

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

**Tags:** rna-seq, wgs

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## 2 answers

### Answer by username_0 on 2017-05-31. Score: 9

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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### Answer by username_1 on 2017-05-31. Score: 0

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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