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- Title
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
- Authors
Chen, Ken; Wallis, John W.; Kandoth, Cyriac; Kalicki−Veizer, Joelle M.; Mungall, Karen L.; Mungall, Andrew J.; Jones, Steven J.; Marra, Marco A.; Ley, Timothy J.; Mardis, Elaine R.; Wilson, Richard K.; Weinstein, John N.; Ding, Li
- 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/BreakFusionContact: kchen3@mdanderson.org; lding@genome.wustl.eduSupplementary information: Supplementary data are available at Bioinformatics online
- Subjects
GENE fusion; BIOINFORMATICS; NUCLEOTIDE sequence; COMPUTER software; SENSITIVITY &; specificity (Statistics); COMPUTATIONAL biology
- Publication
Bioinformatics, 2012, Vol 28, Issue 14, p1923
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bts272