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FusionFinder | A software tool to identify expressed gene fusion candidates from RNA-Seq data

Discovers fusion transcripts and their isoforms. FusionFinder automatically identifies candidate gene fusion partners from single-end (SE) or paired-end (PE) RNA-Seq read data. The alignments generated by the software provide the sequence of the fusion candidate at the point of the transcript breakpoint and also provide details regarding whether or not this sequence retains an open reading frame (ORF).

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FusionFinder classification

FusionFinder specifications

Unique identifier:
OMICS_01349
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
1.2.1
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
Software type:
Package/Module
Restrictions to use:
None
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.
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

FusionFinder distribution

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FusionFinder support

Documentation

Maintainers

  • Richard Francis <>
  • FusionFinder Team <>

Credits

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Publications

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

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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