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

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ID: 116270
2013
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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 .
Reference Key
kim2013genometophat2: Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Daehwan Kim;Geo Pertea;Cole Trapnell;Harold Pimentel;Ryan Kelley;Steven L Salzberg;Daehwan Kim;Geo Pertea;Cole Trapnell;Harold Pimentel;Ryan Kelley;Steven L Salzberg;
Journal Genome biology
Year 2013
DOI
doi:10.1186/gb-2013-14-4-r36
URL
https://doi.org/10.1186%2Fgb-2013-14-4-r36
Keywords
bioinformatics evolutionary biology animal genetics and genomics microbial genetics and genomics plant genetics and genomics human genetics

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