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

Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L. Salzberg

Research output: Contribution to journalArticle

5658 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberR36
JournalGenome Biology
Volume14
Issue number4
DOIs
StatePublished - Apr 25 2013

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gene fusion
Gene Fusion
Transcriptome
transcriptome
RNA
genome
Genome
Pseudogenes
pseudogenes
gene
translocation
genomics
Software
Technology
software
nucleotide sequences
experiment
alignment

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

TopHat2 : Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. / Kim, Daehwan; Pertea, Geo; Trapnell, Cole; Pimentel, Harold; Kelley, Ryan; Salzberg, Steven L.

In: Genome Biology, Vol. 14, No. 4, R36, 25.04.2013.

Research output: Contribution to journalArticle

Kim, Daehwan ; Pertea, Geo ; Trapnell, Cole ; Pimentel, Harold ; Kelley, Ryan ; Salzberg, Steven L. / TopHat2 : Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. In: Genome Biology. 2013 ; Vol. 14, No. 4.
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