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Tophat is part of the tuxedo suite of RNA-Seq tools. Tophat does a transcriptome-aware alignment of the input sequences to a reference genome using either the Bowtie or Bowtie2 aligner (in theory it can use other aligners, but we do not recommend this).
How Tophat Works
Image from: http://genomebiology.com/2013/14/4/R36
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