TopHat swMATH ID: 17157 Software Authors: Kim D, Pertea G, Trapnell C et al Description: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat. Homepage: http://ccb.jhu.edu/software/tophat/index.shtml Related Software: Bioconductor; edgeR; R; KEGG; STAR; RSEM; BLAT; DEseq; HTSeq; FastQC; Galaxy; Soap; EBSeq; ggplot2; Trimmomatic; HISAT; Salmon; Voom; gcrma; limma Cited in: 21 Publications all top 5 Cited by 61 Authors 2 Jiang, Hui 2 Papastamoulis, Panagiotis 2 Rattray, Magnus 1 Akalin, Altuna 1 Attolini, Camille Stephan-Otto 1 Axelson-Fisk, Marina 1 Cai, Yudong 1 Cornwell, Steffen 1 Corrada Bravo, Héctor 1 Cox, Anthony J. 1 Davis, Sean L. 1 Delgado, Alberto Santos 1 Feng, Dai 1 Fernandes, Francisco E. jun. 1 Francisco, Alexandre P. 1 Franke, Verdan 1 Glaus, Peter 1 Gunady, Mohamed K. 1 Hauswedell, Hannes 1 Hensman, James 1 Jakobi, Tobias 1 Johnson, Marla 1 Keith, Jonathan M. 1 Kong, Yan 1 Kroiss, Manuel 1 Li, Jingyi Jessica 1 Li, Wei Vivian 1 Liu, Huaping 1 Lu, Lin 1 Mathé, Ewy 1 Mount, Stephen M. 1 Nguyen, XuanLong 1 Picardi, Ernesto 1 Pietrzak, Maciej 1 Purdom, Elizabeth 1 Rempała, Grzegorz A. 1 Ronen, Jonathan 1 Rosone, Giovanna 1 Rossell, David 1 Ruddy, Sean 1 Salzman, Julia 1 Schulz-Trieglaff, Ole B. 1 Seweryn, Michał T. 1 Song, Wei 1 Stöcker, Almond 1 Teixeira, Andreia Sofia 1 Uyar, Bora 1 von Stechow, Louise 1 Wang, Jiajia 1 Wang, Shaopeng 1 Wesołowski, Jacek 1 Wolff, Alexander 1 Wong, Wing Hung 1 Wu, Weisheng 1 Yin, Xia 1 Yuan, Fei 1 Zang, Weidong 1 Zhang, Shihua 1 Zhang, Yuhang 1 Zhao, Anqi 1 Zhao, Lili all top 5 Cited in 11 Serials 4 Methods in Molecular Biology 3 The Annals of Applied Statistics 2 Statistical Applications in Genetics and Molecular Biology 2 Computational Biology 1 Mathematical Biosciences 1 Statistical Science 1 International Journal of Foundations of Computer Science 1 Test 1 Journal of Theoretical Biology 1 Bayesian Analysis 1 Chapman & Hall/CRC Computational Biology Series all top 5 Cited in 8 Fields 19 Biology and other natural sciences (92-XX) 9 Statistics (62-XX) 3 Computer science (68-XX) 2 General and overarching topics; collections (00-XX) 2 Probability theory and stochastic processes (60-XX) 1 Numerical analysis (65-XX) 1 Operations research, mathematical programming (90-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year