An important task for high throughput sequencing, is mapping the generated reads to the reference sequence. A number of software tools have been proposed to accomplish this task. The review by Fonseca et al compares the mappers available so far. A regaularly updated version of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappers/. The reference of this review article is given below
Fonseca et al (2012) Bioinformatics 28(24)3169-3177