Novoalign is a short-read mapper designed to be fast and sensitive on small to large genome databases. It’s primary design is based on the use of read quality information and the need to assemble genomes from resequencing experiments. Novoalign supports fragment, paired-end and mate-pair reads from major sequencing platforms such as Illumina, SOLiD and Roche 454. NovoalignCS is the version of Novoalign developed for SOLiD colourspace reads.
The full version of Novoalign is a commercial product but a version of Novoalign with some limits to functionality is available for free at: http://www.novocraft.com/main/downloadpage.php