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FusionFinder specifications


Unique identifier OMICS_01349
Name FusionFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data A summary file, which contains a ranked list of fusion candidates based on their evidence strength, a file containing the full details for each isoform of G1 and G2 and the genomic coordinates of the alignment blocks on G1 and G2, with their respective corresponding Ensembl exon IDs, a file that contains a flag denoting the stage at which each read was filtered and statistics detailing the raw numbers of reads that have been filtered at various stages of the algorithm.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability No
Bowtie; Perl Modules: Bio::Perl, Bio::Tools::Run::Alignment::Muscle, Getopt::Long, List::MoreUtils, Pod::Usage, Config::IniFiles, Sort::ArrayOfArrays, Term::ProgressBar, GD::Graph, DBI, DBD::mysql; Ensembl API; Muscle; MySQL; Ensembl Database
Maintained No


No version available



This tool is not available anymore.

Publication for FusionFinder

FusionFinder citations


Systematic chemical and molecular profiling of MLL rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

PMCID: 5220136
PMID: 27443263
DOI: 10.1038/leu.2016.165

[…] rate (idr) package (v1.2) with default settings. analyses were performed using r (v3.1.2). gene ontology enrichment analysis was performed using david. mll-fusion split-reads were identified with fusionfinder using default settings. split-reads containing identical strings of mll- and candidate fusion gene sequences were extracted using ‘grep', searching for chimeric sequences with 15 […]


Comparative assessment of methods for the fusion transcripts detection from RNA Seq data

PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] in the past, some attempts have been made to compare these software packages. in 2013, carrara et al. compared the performance of six fusion detection software tools (i.e. fusionhunter, fusionmap, fusionfinder, mapsplice, defuse, and tophat-fusion) with positive and negative datasets. however, several newly developed tools like breakfusion, soapfuse, jaffa, nfuse, ericscript, and fusioncatcher […]


Novel KAT6B KANSL1 Fusion Gene Identified by RNA Sequencing in Retroperitoneal Leiomyoma with t(10;17)(q22;q21)

PMCID: 4306483
PMID: 25621995
DOI: 10.1371/journal.pone.0117010

[…] quality of the raw sequence data was assessed using fastqc software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). the softwares fusionmap (http://www.omicsoft.com/fusionmap/) [] and fusionfinder (http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/) [] were used for the discovery of fusion transcripts. in addition, the “grep” command […]


The “Grep” Command But Not FusionMap, FusionFinder or ChimeraScan Captures the CIC DUX4 Fusion Gene from Whole Transcriptome Sequencing Data on a Small Round Cell Tumor with t(4;19)(q35;q13)

PMCID: 4064965
PMID: 24950227
DOI: 10.1371/journal.pone.0099439

[…] did not detect a cic-dux4 fusion transcript previously described as the crucial gene-level outcome of this specific translocation. the rna sequencing data were analysed using the fusionmap, fusionfinder, and chimerascan programs which are specifically designed to identify fusion genes. fusionmap, fusionfinder, and chimerascan identified 1017, 102, and 101 fusion transcripts, […]


Comparison between Karyotyping FISH Reverse Transcription PCR and RNA Sequencing Fusion Gene Identification Programs in the Detection of KAT6A CREBBP in Acute Myeloid Leukemia

PMCID: 4010518
PMID: 24798186
DOI: 10.1371/journal.pone.0096570

[…] approach: g-banding was followed by fluorescence in situ hybridization (fish) and reverse transcription pcr (rt-pcr). the second was rna-seq followed by data analysis using fusionmap and fusionfinder programs with special emphasis on candidates located in the 1p13, 8p11, 16p13, and 21q22 breakpoints. fish analysis indicated the presence of a kat6a/crebbp chimera. rt-pcr followed […]


Fusion Transcript Discovery in Formalin Fixed Paraffin Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression

PMCID: 3984112
PMID: 24727804
DOI: 10.1371/journal.pone.0094202

[…] methods are available to detect fusion transcripts from rna-seq paired-end read data (chimeranscan , snowshoes-ftd , gstruct-fusions and gfp ) or single-end read (tophat-fusion , fusionmap and fusionfinder ). all fusion transcript detection methods utilize split reads, in which a single-end read or one read from the pair-end read is mapped to each end of two fused genes exactly […]

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FusionFinder institution(s)
Division of Bioinformatics and Biostatistics, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia; Division of Children’s Leukaemia and Cancer Research, Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia
FusionFinder funding source(s)
Supported by the WA State Government Centres of Excellence Program, the Children’s Leukaemia and Cancer Research Foundation, Perth and the Mike Schon-Hegrad Memorial Fund.

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