FuMa 3.0.0 – Reporting Overlap in RNA-seq Detected Fusion Genes

FuMa 3.0.0

:: 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

Hoogstrate Y, Böttcher R, Hiltemann S, van der Spek PJ, Jenster G, Stubbs AP.
FuMa: reporting overlap in RNA-seq detected fusion genes.
Bioinformatics. 2016 Apr 15;32(8):1226-8. doi: 10.1093/bioinformatics/btv721. Epub 2015 Dec 10. PMID: 26656567.

FuSeq 1.1.4 – Discover Fusion Genes from paired-end RNA Sequencing data

FuSeq 1.1.4

:: DESCRIPTION

FuSeq discovers fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

FuSeq

:: MORE INFORMATION

Citation

Vu TN, Deng W, Trac QT, Calza S, Hwang W, Pawitan Y.
A fast detection of fusion genes from paired-end RNA-seq data.
BMC Genomics. 2018 Nov 1;19(1):786. doi: 10.1186/s12864-018-5156-1. PMID: 30382840; PMCID: PMC6211471.

FusionMap 20180108 – Detecting Fusion Genes from Next-generation Sequencing data at Base-pair Resolution

FusionMap 20180108

:: 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

FusionMap team

:: 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.

ArtiFuse v1.0.0 – Computational Validation of Fusion Gene Detection tools without relying on simulated reads

ArtiFuse v1.0.0

:: DESCRIPTION

ArtiFusion is a tool to simulate artificial fusion events by modifying a given reference genome. The tool copies parts of the exonic sequence of gene A within the reference genome FASTA sequence into the downstream region of gene B and replaces the copied regions of gene A with Ns. The breakpoints are defined by using a size ratio between gene A and gene B and are always placed on exon-exon junctions. Intronic and intergenic regions remain unchanged.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

ArtiFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz613. doi: 10.1093/bioinformatics/btz613.
ArtiFuse – Computational validation of fusion gene detection tools without relying on simulated reads.
Sorn P, Hohlsträter C, Löwer M, Sahin U, Weber D.

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