STAR-Fusion specifications

Information


Unique identifier OMICS_17313
Name STAR-Fusion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Brian Haas <>

Publication for STAR-Fusion

STAR-Fusion in publications

 (11)
PMCID: 5916809
PMID: 29617662
DOI: 10.1016/j.celrep.2018.03.050

[…] developed bioinformatic tools to methodically identify fusion transcripts across the tcga rna-seq data corpus using the institute for systems biology (isb) cancer genomics cloud. these tools include star-fusion, breakfast, and ericscript (star methods). fusion calling across 9,624 tcga tumor samples from 33 cancer types identified a total of 25,664 fusion transcripts, with a 63.3% validation […]

PMCID: 5880266
PMID: 29434027
DOI: 10.1101/mcs.a002618

[…] version 5.3., dnase-treated, ribo-depleted total tumor rna was used as input for library construction using illumina's truseq stranded total rna sample prep. rna-seq data were processed using star-fusion, and these data were used to detect putatively expressed gene fusions in the tumor (https://github.com/star-fusion). we analyzed 125,302,701 rna-seq reads., snpeff and custom in-house […]

PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] <0.01, driver probability >0.99, and minimum support reads >100. in a validation approach we aligned reads with star_2.5.2a in 2-pass mode to the grch37/hg19 reference genome. sub-routine star-fusion was used to evaluate fusion transcripts. general overlap to results obtained by tophat-fusion was quite low (sample-wise: 21/96; global by gene partners: 30/96); however, all prominent […]

PMCID: 5638846
PMID: 29026114
DOI: 10.1038/s41467-017-01026-0

[…] note that we included rearrangement calls only if they were validated by definition at base-pair resolution. rna reads were searched for gene fusion using three different algorithms (tophat-fusion; star-fusion (github.com/star-fusion/star-fusion/wiki); defuse)., we used previously described methods to call driver events. in brief, drivers in recessive cancer genes were called if mutations […]

PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] of various cancer types. rna-seq has been shown as a valuable source for detecting fusion genes. several tools have been proposed to identify fusion from transcriptomic data such as jaffa, star-fusion, tophat-fusion, fusioncatcher, and soapfuse. in addition to these short-read-based techniques, idp-fusion, and iso-seq methods can analyse long-read rna-seq data to identify fused genes., […]


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STAR-Fusion institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Blueprint Medicines, Cambridge, MA, USA; Department of Computer Science, University of California, Berkeley, CA, USA; Grail, Inc., Menlo Park, CA, USA; National Center for Genome Analysis Support, Indiana University, Bloomington, IN, USA; Department of Biology, University of Indiana, Bloomington, IN, USA; Program in Translational Neuro Psychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Medical Oncology, Dana-Farber Cancer Institute; Department of Medicine, Brigham and Women's Hospital; Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
STAR-Fusion funding source(s)
This work has been supported by Howard Hughes Medical Institute, the Klarman Cell Observatory, National Cancer Institute grants 1U24CA180922-01 and 1R50CA211461-01, and National Institutes of Health grant 5U54HG007004-04.

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