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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



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Publication for FusionFinder

FusionFinder citations


KAOS: a new automated computational method for the identification of overexpressed genes

BMC Bioinformatics
PMCID: 5123341
PMID: 28185541
DOI: 10.1186/s12859-016-1188-1

[…] ts. Other methods try to predict fusion genes at the genomic level by checking genes in their transition regions or analyzing Copy Number Variations (CNVs) []. Finally, several tools, such as TopHat, FusionFinder or FusionMap are based on RNASeq data and detect gene fusion candidates by considering the discordant read pairs aligning to two different genes, as reviewed in Carrara et al. []. The mai […]


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

[…] ery 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 nucleoti […]


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

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

[…] he 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 (http://en.wikipedia.org/wi […]


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)

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

[…] cer cells is massively sequenced, and then the raw data are analyzed with one or more programs specifically dedicated to the task of detecting fusion transcripts such as ChimeraScan , FusionMap , and FusionFinder . However, the programs typically identify numerous fusion transcripts making the assessment of which of them are important and which are noise extremely difficult. To overcome this chall […]


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

PLoS One
PMCID: 4010518
PMID: 24798186
DOI: 10.1371/journal.pone.0096570
call_split See protocol

[…] sed for the discovery of fusion transcripts: FusionMap (release date 2012-04-16) together with the pre-built Human B37 and RefGene from the FusionMap website (http://www.omicsoft.com/fusionmap/) and FusionFinder . In addition, the “grep” command (http://en.wikipedia.org/wiki/Grep) was used to search the fastq files of the sequence data (http://en.wikipedia.org/wiki/FASTQ_format). […]


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

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

[…] tics 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 at the fusio […]


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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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