Cufflinks
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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. It creates an overlap graph and then finds the minimum set of transcripts that explain the intron junctions within the reads (minimum path cover of the graph). Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. (http://cufflinks.cbcb.umd.edu/)
