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Gene fusion detection software tools | RNA sequencing data analysis

Gene fusions arising from chromosomal translocations have been implicated in cancer. RNA-seq has the potential to discover such rearrangements generating functional proteins (chimera/fusion). Recently, many methods for chimeras detection have been…
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Segemehl
Desktop

Segemehl

Maps short sequencer reads to reference genomes. Segemehl is a read aligner…

Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced…

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nFuse
Desktop

nFuse

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole…

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

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TopHat-Fusion
Desktop

TopHat-Fusion

An enhanced version with the ability to align reads across fusion points, which…

An enhanced version with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

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INTEGRATE
Desktop

INTEGRATE

Allows identification of gene fusions. INTEGRATE uses both RNA-seq and whole…

Allows identification of gene fusions. INTEGRATE uses both RNA-seq and whole genome sequencing (WGS) encompassing and spanning reads to focus on the discovery of expressed gene fusions. It utilizes…

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chimerascan
Desktop

chimerascan

A software package that detects gene fusions in paired-end RNA sequencing…

A software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

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FusionSeq
Desktop

FusionSeq

Infers candidate fusion transcripts by analyzing paired-end RNA-Seq data.…

Infers candidate fusion transcripts by analyzing paired-end RNA-Seq data. FusionSeq is a standalone software that allows users to detect known and novel fusions and prioritize the candidates thanks…

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FusionAnalyser
Desktop

FusionAnalyser

A package using paired reads and mapping to different genes (Bridge reads), to…

A package using paired reads and mapping to different genes (Bridge reads), to build a data set of candidate fusion events. FusionAnalyser is a graphical, eventdriven tool which makes use of…

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FusionMetaCalle…
Desktop

FusionMetaCaller

A meta-caller algorithm by combining top performing methods to re-prioritize…

A meta-caller algorithm by combining top performing methods to re-prioritize candidate fusion transcripts with high confidence that can be followed by experimental validation. Top performing methods…

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aRNApipe
Desktop

aRNApipe automated RNA-seq pipeline

Provides an integrated and efficient workflow for analyzing single-end and…

Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…

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comrad
Desktop

comrad

Predicts fusion transcripts and their associated genome rearrangements using…

Predicts fusion transcripts and their associated genome rearrangements using low coverage whole genome shotgun sequencing (WGSS) data. Comrad is an algorithmic framework for the integrated analysis…

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ShortFuse
Desktop

ShortFuse

A package for using paired-end reads to find fusion transcripts without…

A package for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing. ShortFuse estimates fusion transcript abundances by considering…

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SnowsShoes-FTD
Desktop

SnowsShoes-FTD

A bioinformatics tool to identify fusion transcripts from paired-end…

A bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data.

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CRAC
Desktop
Web

CRAC Complex Reads Analysis & Classification

An RNA-Seq mapping software tool that include the discovery of transcriptomic…

An RNA-Seq mapping software tool that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in…

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deFuse
Desktop

deFuse

Allows gene fusion discovery using RNA-Seq data. Defuse’s aim is to guide a…

Allows gene fusion discovery using RNA-Seq data. Defuse’s aim is to guide a dynamic programming-based split read analysis with discordant paired end alignments. The software employs heuristic…

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FuGePrior
Desktop

FuGePrior

Prioritizes of gene fusions from paired-end RNA-Seq data. FuGePrior combines…

Prioritizes of gene fusions from paired-end RNA-Seq data. FuGePrior combines state of the art tools for chimeric transcript discovery and prioritization, a series of filtering and processing steps…

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PRADA
Desktop

PRADA

A pipeline to analyze paired end RNA-Seq data to generate gene expression…

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

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FusionMap
Desktop

FusionMap

An efficient fusion aligner which aligns reads spanning fusion junctions…

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions.

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Fusion-sense
Desktop

Fusion-sense

Uses to calculate the estimated sensitivity of fusion finding for an RNA-seq…

Uses to calculate the estimated sensitivity of fusion finding for an RNA-seq experiment. Fusion-sense plots the estimated sensitivity as a function of the distance to the 3’ end and calculates the…

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FusionCatcher
Desktop

FusionCatcher

Searches for novel/known somatic fusion genes, translocations, and chimeras in…

Searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased…

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R453Plus1Toolbo…
Desktop

R453Plus1Toolbox

Provides an interface to access 454 Sequencing data processed with Roche GS FLX…

Provides an interface to access 454 Sequencing data processed with Roche GS FLX Software from within R and offers many tools for quality reports, annotation and advanced analyses. Users can add…

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NCLscan
Desktop

NCLscan

A high accurate method for detecting intragenic and intergenic non-co-linear…

A high accurate method for detecting intragenic and intergenic non-co-linear (NCL) transcripts. NCLscan utilizes a stepwise alignment strategy to almost completely eliminate false calls (>98%…

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InFusion
Desktop

InFusion

A toolkit for fusion gene and chimeric transcript detection from RNA-seq data.…

A toolkit for fusion gene and chimeric transcript detection from RNA-seq data. InFusion is a computational method for the discovery of chimeric transcripts from RNA-seq data capable of detecting…

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ChimeRScope
Web
Desktop

ChimeRScope

Inspects the k-mer contents of the RNA-Seq paired-end reads for fusion…

Inspects the k-mer contents of the RNA-Seq paired-end reads for fusion transcript detection. ChimeRScope is an alignment-free method which uses large-scale fusion transcript data analysis. It could…

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JAFFA
Desktop

JAFFA

A sensitive fusion detection method that out-performs other methods with reads…

A sensitive fusion detection method that out-performs other methods with reads of 100 bp or greater. JAFFA is based on the idea of comparing a transcriptome (e.g. in a cancer sample) against a…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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TRUP
Desktop

TRUP Tumor-specimen suited RNA-seq Unified Pipeline

A pipeline designed for analyzing RNA-seq data from tumor samples. As an…

A pipeline designed for analyzing RNA-seq data from tumor samples. As an unified pipeline, TRUP is designed to sensitively and accurately dissect the complexity of the cancer transcriptome by…

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FusionHunter
Desktop

FusionHunter

Identifies fusion transcripts from transcriptional analysis of paired-end…

Identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset.…

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

Automates RNA-seq processing, integration and analysis. SePIA allows…

Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a…

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wapRNA
Desktop
Web

wapRNA

This is a free web-based application for the processing of high-throughput…

This is a free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of…

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VFS
Desktop

VFS ViralFusionSeq

A versatile high-throughput sequencing (HTS) tool for discovering viral…

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution.

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Bellerophontes
Desktop

Bellerophontes

A fully automated framework for the detection of novel fusion transcripts in…

A fully automated framework for the detection of novel fusion transcripts in paired end RNA-Seq data.

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IDP-fusion
Desktop

IDP-fusion

An innovative hybrid sequencing approach to detect fusion genes, determine…

An innovative hybrid sequencing approach to detect fusion genes, determine fusion sites and identify and quantify fusion isoforms. IDP-fusion is the first method to study gene fusion events by…

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FuMa
Desktop

FuMa FusionMatcher

Reports identical fusion genes based on gene-name annotations. FuMa…

Reports identical fusion genes based on gene-name annotations. FuMa automatically compares and summarizes all combinations of two or more datasets in a single run, without additional programming…

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Chimera
Desktop

Chimera

Allows users to manipulate, analyze and filter fusion events detected by a…

Allows users to manipulate, analyze and filter fusion events detected by a variety of fusion detection tools. Chimera performs a first step of validation, which can be useful given the high number of…

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FusionFinder
Desktop

FusionFinder

A perl-based software package, which can be used to find fusion transcript…

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

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SOAPfusion
Desktop

SOAPfusion

Allows fusion discovery with paired-end RNA-Seq reads. SOAPfusion identifies…

Allows fusion discovery with paired-end RNA-Seq reads. SOAPfusion identifies fusion transcripts with RNA-Seq reads. The software integrates a specially designed SOAPfusion-aligner to perform both…

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GFusion
Desktop

GFusion

Improves the sensitivity and specifcity of fusion detection. GFusion is a…

Improves the sensitivity and specifcity of fusion detection. GFusion is a powerful and efficient method for both paired-end and single-end RNA-seq data. It predicts fusion genes by comprehensive…

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SQUID
Desktop

SQUID

Predicts transcriptomic structural variants (TSVs) from RNA-seq data. SQUID is…

Predicts transcriptomic structural variants (TSVs) from RNA-seq data. SQUID is a computational tool that divides the reference genome into segments and builds a genome segment graph from both…

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confFuse
Desktop

confFuse

Assigns each putative fusion transcript a confidence score. confFuse is a…

Assigns each putative fusion transcript a confidence score. confFuse is a scoring algorithm that can be applied on paired-end RNA-seq across tumor entities with both high sensitivity and high…

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pizzly
Desktop

pizzly

Serves for gene fusion discovery. Pizzly filters false positives using…

Serves for gene fusion discovery. Pizzly filters false positives using biologically-relevant heuristics. This tool is able to assemble transcripts at breakpoint resolution and quantify fusion…

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IM-Fusion
Desktop

IM-Fusion

Identifies transposon insertions from splicing events between endogenous genes…

Identifies transposon insertions from splicing events between endogenous genes and the transposon. IM-Fusion identifies exactly which gene(s) are affected by a transposon insertion and how the…

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STAR-Fusion
Desktop

STAR-Fusion

Uses the STAR aligner to identify candidate fusion transcripts supported by…

Uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It performs a fast…

COPA
Desktop

COPA Cancer Outlier Profile Analysis

Finds genes undergoing recurrent fusion in a given cancer type by finding pairs…

Finds genes undergoing recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. COPA is intended to find pairs of genes that may be involved in…

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Dissect
Desktop

Dissect

A transcriptome-to-genome alignment tool, which can identify and characterize…

A transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

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SnowShoes-FTD
Desktop

SnowShoes-FTD

A bioinformatics tool to identify fusion transcripts from paired-end…

A bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. SnowShoes-FTD employs multiple steps of false positive filtering to nominate fusion transcripts…

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ChimPipe
Desktop

ChimPipe

A modular and easy-to-use method to reliably identify chimeras from paired-end…

A modular and easy-to-use method to reliably identify chimeras from paired-end Illumina RNA-seq data. ChimPipe identifies exact junction coordinates for both kinds of datasets, and shows the best…

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EricScript
Desktop

EricScript chimEric tranScript detection algorithm

A computational framework for the discovery of gene fusions in paired end…

A computational framework for the discovery of gene fusions in paired end RNA-seq data. It is able to generate synthetic gene fusions by using the EricScript simulator and calculate a number of…

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Pegasus
Desktop

Pegasus

A pipeline for the annotation and prediction of biologically functional gene…

A pipeline for the annotation and prediction of biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, reconstruction of novel…

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FusionQ
Desktop

FusionQ

A fusion detection tool based on paired-end RNA-Seq data. This tool can detect…

A fusion detection tool based on paired-end RNA-Seq data. This tool can detect gene fusions, construct the structures of chimerical transcripts, and estimate their abundances. FusionQ employs a new…

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PAVFinder
Desktop

PAVFinder Post Assembly VariantFinder

Identifies structural variants from de novo assemblies. PAVFinder is able to…

Identifies structural variants from de novo assemblies. PAVFinder is able to detect translocations, inversions, duplications, insertions, deletions, simple-repeat expansions/contractions for genomic…

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Hera
Desktop

Hera

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides…

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides (i) base-to-base alignment BAM file, (ii) transcript abundance estimation, and (iii) fusion gene detection with fused…

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QRNAseq
Desktop

QRNAseq

A tool to manage huge amounts of RNA-seq data in an integrative way which…

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…

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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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Array Studio
Desktop

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

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SOAPfuse
Desktop

SOAPfuse

An open source tool developed for genome-wide detection of fusion transcripts…

An open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data.

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BreakFusion
Desktop

BreakFusion

Provides a targeted assembly approach for novel transcriptomic sequence…

Provides a targeted assembly approach for novel transcriptomic sequence discovery. BreakFusion is a Next-Generation Sequencing (NGS) Bioinformatics pipeline that consists of five steps: (i)…

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