FuMa – Reporting Overlap in RNA-seq Detected Fusion Genes

FuMa

:: DESCRIPTION

FuMa (Fusion Matcher) is a program that reports identical fusion genes based on gene-name annotations.

::DEVELOPER

FuMa team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuMa

:: MORE INFORMATION

Citation

FuMa: reporting overlap in RNA-seq detected fusion genes.
Hoogstrate Y, B?ttcher R, Hiltemann S, van der Spek P, Jenster G, Stubbs AP.
Bioinformatics. 2015 Dec 10. pii: btv721

FusionMap 20150331 – Detecting Fusion Genes from Next-generation Sequencing data at Base-pair Resolution

FusionMap 20150331

:: DESCRIPTION

FusionMap is an efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies

::DEVELOPER

OmicSoft Corporation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 FusionMap

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):1922-8. Epub 2011 May 18.
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W.

iFUSE – Structural Variants from Next Generation Sequencing data

iFUSE

:: DESCRIPTION

iFUSE is a web-based fusion gene explorer. Upload your Complete Genomics junctions files, or your FusionMap FusionReport.txt file, and iFUSE will analyze and visualize your fusion gene candidates, and report the resulting sequences on the DNA, RNA and protein levels.

::DEVELOPER

ErasmusMC Bioinformatics Department

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Apache
  • PHP
  • MySQL
  • SED & AWK

:: DOWNLOAD

 iFUSE

:: MORE INFORMATION

Citation:

iFUSE: integrated fusion gene explorer.
Hiltemann S, McClellan EA, van Nijnatten J, Horsman S, Palli I, Teles Alves I, Hartjes T, Trapman J, van der Spek P, Jenster G, Stubbs A.
Bioinformatics. 2013 Jul 1;29(13):1700-1. doi: 10.1093/bioinformatics/btt252.

QRNAseq 0.1.0 – for Functional Isoform, Driver Mutation Gene and Fusion Gene Detection

QRNAseq 0.1.0

:: DESCRIPTION

QRNAseq is a tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function analysis. The QRNAseq system comprises pipelines that load input, analyzes the NGS data, exports outputs into a relational database, integrates and mines the data with other data types, and generates key gene signatures of interest.

::DEVELOPER

Center for Bioinformatics & Systems Biology, The Methodist Hospital Research Institute.

:: SCREENSHOTS

QRNAseq

:: REQUIREMENTS

  • Linux/ WIndows
  • C++
  • QT4

:: DOWNLOAD

 QRNAseq

:: MORE INFORMATION