Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Ken Chen, John W. Wallis, Cyriac Kandoth, Joelle M. Kalicki-veizer, Karen L. Mungall, Andrew J. Mungall, Steven J. Jones, Marco A. Marra, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, John N. Weinstein, Li Ding

Research output: Contribution to journalArticlepeer-review

46 Scopus citations

Abstract

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.

Original languageEnglish
Article numberbts272
Pages (from-to)1923-1924
Number of pages2
JournalBioinformatics
Volume28
Issue number14
DOIs
StatePublished - Jul 2012

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