Publication

BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data.

Bioinformatics. 2012 May 4. [Epub ahead of print]

Abstract

SUMMARY: 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
CONTACT: kchen3@mdandesron.org or Li Ding.

Authors

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.