FusionFinder protocols

View FusionFinder computational protocol

FusionFinder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene fusion detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

FusionFinder specifications

Information


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
Requirements
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

Versioning


Add your version

Documentation


Maintainers


This tool is not available anymore.

Publication for FusionFinder

FusionFinder in pipeline

2016
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 […]


To access a full list of citations, you will need to upgrade to our premium service.

FusionFinder in publications

 (8)
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 […]

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 […]

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 […]

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, […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

FusionFinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review FusionFinder