components_and_similar_projects

Component and Similar Projects

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data - PMID: 26582927
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. - PMID: 26862001

Selected tools include:

IGV
Ribbon
Packages like chimeraviz also have visualizations
Packages like circlize are adaptable for this (as well as other Bioconductor packages)
svviz - Read visualizer for structural variants

Computational inference:
- 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
Databases:
- CIViC
- Database of Genomic Variants
- Atlas of Genetics and Cytogenetics in Oncology and Haematology
- Tumor Fusion Gene Data Portal
- Recount
  - Note that this is actually an interface for downloading fusion junctions from many SRA studies
- ChimerDB
- TICdb
- COSMIC
- dbCRID
  - Note - download links seem broken here
- ChiTars
- Archer's quiver DB - Note that this aggregates many of the above sources (but is not directly queryable)
Other annotation tools:
- FusionAnnotator

MetaSV
- Bioinformatics Article
- Mainly focused on large-scale structural variants, from tools like Pindel, BreakDancer, CNVnator, BreakSeq2
confFuse
- GitHub link
- Frontiers in Genetics Article
chimeraviz
- Bioinformatics Application Note
- BioConductor
- 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MAVIS - BCGSC unpublished tool along similar lines