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      TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

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          Abstract

          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.

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          Author and article information

          Contributors
          Journal
          Genome Biol
          Genome Biol
          Genome Biology
          BioMed Central
          1465-6906
          1465-6914
          2013
          25 April 2013
          : 14
          : 4
          : R36
          Affiliations
          [1 ]Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
          [2 ]Department of Computer Science, University of Maryland, College Park, MD 20742, USA
          [3 ]Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
          [4 ]Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
          [5 ]Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
          [6 ]Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., Cambridge, MA, 02142, USA
          [7 ]Department of Electrical Engineering and Computer Science, University of California, 101 Sproul Hall, Berkeley, CA, 94720, USA
          [8 ]Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
          Article
          gb-2013-14-4-r36
          10.1186/gb-2013-14-4-r36
          4053844
          23618408
          Copyright © 2013 Kim et al.; licensee BioMed Central Ltd.

          This is an open access article distributed under the terms of the Creative Commons Attribution License

          Categories
          Method

          Genetics

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