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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Nat Protoc. 2012 Mar 1;7(3):562–578. doi: 10.1038/nprot.2012.016

Figure 1.

Figure 1

Software components used in this protocol. Bowtie33 forms the algorithmic core of TopHat, which aligns millions of RNA-seq reads to the genome per CPU hour. TopHat's read alignments are assembled by Cufflinks and its associated utility program to produce a transcriptome annotation of the genome. Cuffdiff quantifies this transcriptome across multiple conditions using the TopHat read alignments. CummeRbund helps users rapidly explore and visualize the gene expression data produced by Cuffdiff, including differentially expressed genes and transcripts.