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

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Documentation


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Publication for FusionFinder

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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