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

Bioinformatics
Ken ChenLi Ding

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

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Citations

Feb 15, 2013·Biological Procedures Online·Derek Shyr, Qi Liu
Aug 27, 2013·Genome Biology·Ken ChenLi Ding
Jul 9, 2014·Nature Reviews. Genetics·Li DingBenjamin J Raphael
Jan 14, 2016·BMC Bioinformatics·Osagie G IzuoguMichael S Jackson
Nov 6, 2015·International Journal of Genomics·Inanç BirolRené L Warren
Oct 10, 2015·Database : the Journal of Biological Databases and Curation·Manonanthini Thangam, Ramesh Kumar Gopal
Mar 4, 2014·Current Opinion in Genetics & Development·Jianjiong GaoNikolaus Schultz
Jun 2, 2015·Nature Communications·Alexej AbyzovMark B Gerstein
Apr 24, 2016·Nucleic Acids Research·Natasha S Latysheva, M Madan Babu
Sep 18, 2012·Cell·Ramaswamy GovindanRichard K Wilson
Aug 4, 2016·Wiley Interdisciplinary Reviews. RNA·Shailesh KumarHui Li
Aug 9, 2016·Cell Reports·Adam ShlienPeter J Campbell
Dec 3, 2016·PloS One·Konstantin OkonechnikovFernando Garcia-Alcalde
Jan 30, 2013·Nature Reviews. Genetics·Niranjan Nagarajan, Mihai Pop
Nov 2, 2018·BMC Genomics·Trung Nghia VuYudi Pawitan
Oct 21, 2018·Genome Biology·Ye YuJinze Liu
Sep 13, 2019·Bioinformatics·Xiao YangEarl Hubbell
Oct 15, 2019·Genomics & Informatics·Pora KimSanghyuk Lee
Jun 8, 2017·Wiley Interdisciplinary Reviews. RNA·Katarzyna ChwaleniaHui Li
Dec 7, 2013·Genome Research·Ken ChenGeorge Weinstock
Nov 12, 2015·Genome Research·Jin ZhangChristopher A Maher

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