# Component and Similar Projects

## Recent Review Papers

- Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data - [PMID: 26582927](https://www.ncbi.nlm.nih.gov/pubmed/26582927)
- Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. - [PMID: 26862001](https://www.ncbi.nlm.nih.gov/pubmed/26862001)

## Fusion Callers

Selected tools include:

- trans-ABySS
- deFuse
- FusionCatcher
- EricScript
- pizzly
- Bellerophontes
- InFusion
- JAFFA
- FusionMap
- PRADA
- SOAPfuse 
- STAR-FUSION

## Visualization

- [IGV](http://software.broadinstitute.org/software/igv/)
- [Ribbon](http://genomeribbon.com/)
- Packages like chimeraviz also have visualizations
- Packages like [circlize](https://github.com/jokergoo/circlize) are adaptable for this (as well as other Bioconductor packages)
- [svviz](https://github.com/svviz/svviz) - Read visualizer for structural variants

## Annotation

- Computational inference:
    - [OncoFuse](https://github.com/mikessh/oncofuse)
        - 'Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation.'
        - [PMID: 23956304](https://www.ncbi.nlm.nih.gov/pubmed/23956304)
- Databases: 
    - [CIViC](https://civic.genome.wustl.edu/home)
    - [Database of Genomic Variants](http://dgv.tcag.ca/dgv/app/home)
    - [Atlas of Genetics and Cytogenetics in Oncology and Haematology](http://atlasgeneticsoncology.org/)
    - [Tumor Fusion Gene Data Portal](http://54.84.12.177/PanCanFusV2/)
    - [Recount](https://www.biorxiv.org/content/early/2016/08/08/068478)
        - Note that this is actually an interface for downloading fusion junctions from many SRA studies
    - [ChimerDB](http://203.255.191.229:8080/chimerdbv31/mindex.cdb)
    - [TICdb](http://www.unav.es/genetica/TICdb/)
    - [COSMIC](http://cancer.sanger.ac.uk/cosmic)
    - [dbCRID](http://c1.accurascience.com/dbCRID/)
        - Note - download links seem broken here
    - [ChiTars](http://chitars.bioinfo.cnio.es/)
    - [Archer's quiver DB](http://archerdx.com/software/quiver) - Note that this aggregates many of the above sources (but is not directly queryable)
- Other annotation tools:
    - [FusionAnnotator](https://github.com/FusionAnnotator/FusionAnnotator)

## Aggregation

- MetaSV
    - [Bioinformatics Article](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv204)
    - Mainly focused on large-scale structural variants, from tools like Pindel, BreakDancer, CNVnator, BreakSeq2
- [confFuse](https://www.frontiersin.org/articles/10.3389/fgene.2017.00137/full) 
    - [GitHub link](https://github.com/Zhiqin-HUANG/confFuse)
    - [Frontiers in Genetics Article](https://www.frontiersin.org/articles/10.3389/fgene.2017.00137/full)
- [chimeraviz](https://github.com/stianlagstad/chimeraviz)
    - [Bioinformatics Application Note](https://academic.oup.com/bioinformatics/article/33/18/2954/3835381/chimeraviz-a-tool-for-visualizing-chimeric-RNA)
    - [BioConductor](https://bioconductor.org/packages/release/bioc/html/chimeraviz.html)
    - `chimeraviz` is able to import fusion results from 'nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION'
    - These are imported as R S4 objects. There are then a selection of functions for visualizing and comparing events (from what I can tell the comparison is mostly done at the coordinate level) 
- MAVIS - BCGSC unpublished tool along similar lines

## Simulated Data Sets

- [ICGC-TCGA DREAM Somatic Mutation Calling Challenge - RNA](https://www.synapse.org/#!Synapse:syn2813589/wiki/401435)