Tag: Gene Fusion

FusionFinder 1.2.1 – Finding Gene Fusions In RNA-Seq Data

FusionFinder 1.2.1

:: DESCRIPTION

FusionFinder is a perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.

::DEVELOPER

Richard Francis

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Perl
  • MySQL

:: DOWNLOAD

 FusionFinder

:: MORE INFORMATION

Citation

Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, et al. (2012)
FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data.
PLoS ONE 7(6): e39987. doi:10.1371/journal.pone.0039987

Chimerascan 0.4.5a – Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets

Chimerascan 0.4.5a

:: DESCRIPTION

Chimerascan is a  software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

::DEVELOPER

The Michigan Center for Translational Pathology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Chimerascan

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Oct 15;27(20):2903-4. Epub 2011 Aug 11.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.

BreakFusion 1.0.1 – Identify Gene Fusions from paired-end RNA-Seq data

BreakFusion 1.0.1

:: DESCRIPTION

BreakFusion is a software that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 BreakFusion

:: MORE INFORMATION

Citation:

Ken Chen et al.
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Bioinformatics (2012) 28 (14): 1923-1924.

BreakTrans 0.0.6 – Uncover the Genomic Architecture of Gene Fusions

BreakTrans 0.0.6

:: DESCRIPTION

BreakTrans is a computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 BreakTrans

:: MORE INFORMATION

Citation

Genome Biol. 2013 Aug 23;14(8):R87.
BreakTrans: uncovering the genomic architecture of gene fusions.
Chen K1, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L.

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 – Gene Fusion Discovery using Whole Genome and Transcriptome data

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1

:: DESCRIPTION

INTEGRATE is a tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

INTEGRATE-Neo is a tool for gene fusion neoantigen discovering tool using next-generation sequencing data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

INTEGRATE / INTEGRATE-Neo

:: MORE INFORMATION

Citation

Zhang J, Mardis ER, Maher CA.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PMID: 27797777; PMCID: PMC5408800.

Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PMID: 26556708; PMCID: PMC4691743.

FusionAnalyser – Detect Gene Fusions from paired-end RNA-Seq data

FusionAnalyser

:: DESCRIPTION

FusionAnalyser is a software for detecting gene fusions from paired-end RNA-Seq data.FusionAnalyser uses paired reads mapping to different genes (Bridge reads),  generated through high-throughput whole transcriptome sequencing, to build a first dataset of candidate fusion events. Subsequently, a second dataset, built upon those reads where only one of the two sequences in a pair is successfully mapped to the reference genome (‘Half-mapped Anchor reads’), is generated. The mapped reads in the latter dataset are used as an anchor to tie each Half-mapped event to the corresponding Bridge region.

::DEVELOPER

Rocco Piazza 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 FusionAnalyser 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Sep 1;40(16):e123. Epub 2012 May 8.
FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.
Piazza R, Pirola A, Spinelli R, Valletta S, Redaelli S, Magistroni V, Gambacorti-Passerini C.

deFuse 0.8.2 – Gene Fusion Discovery using RNA-Seq Data

deFuse 0.8.2

:: DESCRIPTION

deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. A classifier trained on real fusions and false positives is applied to the assembled sequences. The software produces a fully annotated output for each predicted fusion. The software is designed to be run out of the box with little configuration, and is compatible SGE, PBS and LSF compute clusters.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 deFuse

:: MORE INFORMATION

Citation

McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, et al. (2011)
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
PLoS Comput Biol 7(5): e1001138. doi:10.1371/journal.pcbi.1001138

LongGF v0.1.2 – Detection of Gene Fusion by long-read Transcriptome Sequencing

LongGF v0.1.2

:: DESCRIPTION

LongGF is a fast computational tool to efficiently detect candidate gene fusion from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • C++

:: DOWNLOAD

LongGF

:: MORE INFORMATION

Citation

Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K.
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
BMC Genomics. 2020 Dec 29;21(Suppl 11):793. doi: 10.1186/s12864-020-07207-4. PMID: 33372596; PMCID: PMC7771079.

ShortFuse 0.2 – Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs

ShortFuse 0.2

:: DESCRIPTION

ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.

::DEVELOPER

Marcus Kinsella

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShortFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1068-75. Epub 2011 Feb 16.
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.