Tophat: First widely used spliced-aware read mapper. Current version is Tophat2
HISAT: Successor to Tophat2. Similar functionality, but n=much more computationally efficient
STAR: Much faster than Tophat, but requires a large amount of memort (30 Gb for human genome)
TopHat [Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11.] TopHat2 [Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.] SpliceMap [Au KF, Jiang H, Lin L, Xing Y, Wong WH. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 2010;38(14):4570–8.] GSNAP [Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010;26(7):873–81.]