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

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 ana...

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Bibliographic Details
Published inBioinformatics Vol. 28; no. 14; pp. 1923 - 1924
Main Authors KEN CHEN, WALLIS, John W, WILSON, Richard K, WEINSTEIN, John N, LI DING, KANDOTH, Cyriac, KALICKI-VEIZER, Joelle M, MUNGALL, Karen L, MUNGALL, Andrew J, JONES, Steven J, MARRA, Marco A, LEY, Timothy J, MARDIS, Elaine R
Format Journal Article
LanguageEnglish
Published Oxford Oxford University Press 15.07.2012
Subjects
Applications Note
Biological and medical sciences
Cell Line, Tumor
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
General aspects
Humans
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Sequence Alignment
Sequence Analysis, RNA - methods
Software
Transcriptome
Target
Data
Identification
Sequencing
Hybrid gene
Transcriptome
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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. http://bioinformatics.mdanderson.org/main/BreakFusion
Bibliography:ObjectType-Article-1
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Associate Editor: Michael Brudno
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/bts272