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TopHat
TopHat is a fast splice junction mapper for RNA-seq reads that can only be used with Bowtie or Bowtie2. TopHat uses Bowtie or Bowtie2 to map RNA-seq reads, and then it analyzes the mapping results to identify splice junctions between exons.
For more information, see http://ccb.jhu.edu/software/tophat/index.shtml.