FusionCatcher pipeline

FusionCatcher specifications

Information


Unique identifier OMICS_01348
Name FusionCatcher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Sara Kangaspeska <>

Publication for FusionCatcher

FusionCatcher IN pipelines

 (4)
2018
PMCID: 5818080
PMID: 29419396
DOI: 10.1242/dmm.031716

[…] generate dendrograms, samples were clustered according to their gene expression profiles using the hclust function in r (r development core team, 2013). candidate fusion genes were identified with fusioncatcher software (fusioncatcher.py 0.99.3e beta) (nicorici et al., 2014). for human exome capture sequencing, the sure select target enrichment system capture process was used with illumina […]

2017
PMCID: 5557398
PMID: 28806978
DOI: 10.1186/s13045-017-0515-y

[…] (additional file 1: table s2). detailed information of rna sequencing and computational analysis is provided in additional file 2., fusion genes were detected using a two-pronged approach. first, fusioncatcher v0.99.4a beta was used to screen for novel and known fusion genes in an unbiased manner (de novo search) [23]. next, we screened a set of predefined established fusion genes […]

2017
PMCID: 5557398
PMID: 28806978
DOI: 10.1186/s13045-017-0515-y

[…] counting uniquely aligned reads supporting the fusion gene (additional file 3: fig. s1, additional file 1: table s4). to reduce false positives, a filtering process of the fusion genes detected by fusioncatcher was applied. these measures consisted of removing fusion genes that met any of the following criteria: blacklisted fusion genes based on reference data provided by fusioncatcher […]

2017
PMCID: 5557398
PMID: 28806978
DOI: 10.1186/s13045-017-0515-y

[…] genes detected by fusioncatcher was applied. these measures consisted of removing fusion genes that met any of the following criteria: blacklisted fusion genes based on reference data provided by fusioncatcher (additional file 1: table s3), fusion genes with fusion-supporting reads that map to multiple genomic locations indicative of sequence homology (common mapping reads), fusion genes […]

FusionCatcher institution(s)
Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland

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