Table 1.
Available fusion annotation and prioritization tools
| Tools | Software implementation | Compatible fusion algorithms | Annotations | Prioritization | Visualization | Code availability | Last Updated |
|---|---|---|---|---|---|---|---|
| annoFuse | R | Arriba, STAR-Fusion for annoFuse; agnostic for shinyFuse | Protein Domains, Kinase, Transcription Factor, Oncogene, Tumor Suppressor Gene, Kinase Domain Retention, Reciprocality, CTAT_HumanFusionLib, Gene Homolog, Expression | Based on quality/artifact filtering, functional, and oncogenic annotation | Genomic view of single or multiple fusion events() with domains, Recurrent fusions and recurrently fused genes barplots | https://github.com/d3b-center/annoFuse/ | September 2020+ |
| AGFusion | Python | Algorithm agnostic; requires two fusion gene partners (gene symbol, Ensembl ID, or Entrez gene ID), predicted fusion junctions in genomic coordinates, genome build | Protein domains | Amino acid structure of fusion | https://github.com/murphycj/AGFusion | September 2019 | |
| chimera | R package | chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher | Uses Oncofuse to prioritize oncogenic fusions | https://rdrr.io/bioc/chimera/ | March 2015 | ||
| chimeraviz | R package | deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPFuse, STAR-Fusion | Genomic view of fusion event (Breakpoints required) | https://github.com/stianlagstad/chimeraviz | October 2019 | ||
| co-Fuse | R | FusionCatcher, SoapFuse, TopHat, DeFuse | Recurrence detection | https://github.com/sakrapee/co-fuse | May 2017 | ||
| FusionAnnotator | perl | Algorithm agnostic; requires fusion gene partners | CTAT_HumanFusionLib, Gene Homolog | https://github.com/FusionAnnotator/FusionAnnotator | July 2019 | ||
| FusionHub | web-based | Algorithm agnostic; requires fusion gene partners to search databases for fusion and uses breakpoints from ChimerSeq to visualize | Utilizes oncofuse for oncogenicity | Circos, domain, network view of fusions | https://fusionhub.persistent.co.in/ | June 2018 | |
| FusionPathway | R | Algorithm agnostic; Fusion gene Entrez IDs and gene symbols, Pfam protein domain IDs of parental genes | Oncogenic pathway association using GSEA | https://github.com/perwu/FusionPathway/ | September 2019 | ||
| Oncofuse | Java/Groovy | Tophat-fusion and TopHat2, FusionCatcher, RNASTAR | Protein domains, expression | Bayesian probability of oncogenicity | https://github.com/mikessh/oncofuse | February 2016 | |
| Pegasus | Java/Perl/Python/Bash | chimerascan 0.4.5, defuse 0.4.3, bellerophontes 0.4.0 | Kinase, Protein domains | Driver Score for oncogenicity | https://github.com/RabadanLab/Pegasus | February 2016 | |
| confFuse | Python | deFuse | Feature dependent scoring | https://github.com/Zhiqin-HUANG/confFuse | November 2017 |
List of ten openly-available fusion annotation and prioritization software tools, compared to annoFuse. Only AGFusion, FusionAnnotator, Fusion Pathway, and certain functions of FusionHub are algorithm agnostic, and most algorithms require outdated fusion algorithm input