title: BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
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.
  
  
  BACKGROUND
  http://bioinformatics.mdanderson.org/main/BreakFusion
authors.affiliation: Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA. kchen3@mdanderson.org
authors.forename: Ken
authors.initials: K
authors.lastname: Chen
authors.forename: John W
authors.initials: JW
authors.lastname: Wallis
authors.forename: Cyriac
authors.initials: C
authors.lastname: Kandoth
authors.forename: Joelle M
authors.initials: JM
authors.lastname: Kalicki-Veizer
authors.forename: Karen L
authors.initials: KL
authors.lastname: Mungall
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Mungall
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Jones
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Ley
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: John N
authors.initials: JN
authors.lastname: Weinstein
authors.forename: Li
authors.initials: L
authors.lastname: Ding
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome