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BreakFusion

BreakFusion

BreakFusion is a tool to identify gene fusions in whole transcriptome paired-end sequencing data. The BreakFusion algorithm uses a combination of alignment strength and paired-end read alignment analyses.

Topic

Assembly; RNA-seq; Genetics; RNA-seq; RNA

Details

  • Operation: Sequence assembly; Alignment; Analysis
  • Software interface: Command-line user interface
  • Language: C++, Perl
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: -
  • Version name: 1.0
  • Credit: The Cancer Center Support Grant from NCI, Center for Large-Scale Genome Sequencing and Analysis, NHGRI, Structural Genomic Variation analysis for the 1000 Genome project, NHGRI.
  • Contact: Ken Chen kchen3 _at_ mdanderson.org
  • Collection: -

Publications

Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L "BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data." Bioinformatics 2012; 28(14):1923-4 https://doi.org/10.1093/bioinformatics/bts272
PMID: 22563071
PMCID: PMC3389765


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