TopHat is a fast splice mapper for RNA-Seq readings. It makes a conscious transcriptome alignment of the input sequences to a reference genome using the Bowtie2 ultra-high performance short reading aligner, and then analyzes the mapping results to identify the splice joints between exons.
It can align readings of various lengths produced by the latest sequencing technologies, while allowing indels of variable length with respect to the reference genome. In addition to new splice alignment, TopHat2 can align readings through fusion breaks, which can occur after genomic translocations.
It combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and precise alignments, even for highly repetitive genomes or in the presence of pseudogenes.