TopHat is a tool for splice-aware mapping of RNA-seq reads. The TopHat uses the Bowtie short read aligner tool (BWT-based algorithm) for the mapping whereafter it identifies intron-exon (splice) junctions. TopHat can use paired-end sequencing reads and parallel computation. (*BWT=Burrows–Wheeler transform)
RNA-seq; Mapping
Trapnell C, Pachter L, Salzberg SL "TopHat: discovering splice junctions with RNA-Seq." Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16. https://doi.org/10.1093/bioinformatics/btp120
PMID: 19289445
PMCID: PMC2672628
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