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Bioinformatics. 2012 Jul 15;28(14):1923-4. doi: 10.1093/bioinformatics/bts272. Epub 2012 May 4.

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

Author information

  • 1Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA. kchen3@mdanderson.org

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.

AVAILABILITY:

http://bioinformatics.mdanderson.org/main/BreakFusion

PMID:
22563071
[PubMed - indexed for MEDLINE]
PMCID:
PMC3389765
Free PMC Article

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