BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

K. Chen, J. W. Wallis, C. Kandoth, J. M. Kalicki-Veizer, K. L. Mungall, A. J. Mungall, S. J. Jones, M. A. Marra, T. J. Ley, E. R. Mardis, R. K. Wilson, J. N. Weinstein (+1 others)
2012 Bioinformatics  
Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency. Availability: http://bioinformatics.mdanderson.org/main/BreakFusion
doi:10.1093/bioinformatics/bts272 pmid:22563071 pmcid:PMC3389765 fatcat:lqcrkcifwzaslch7oltqtzkw74