Accurate mapping of short color-space reads; SHRiMP2 uses seeds computed by SpEED
SHRiMP can be downloaded from this webpage
#CITE
M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, SHRiMP2: Sensitive yet practical short read mapping, Bioinformatics 27(7) (2011) 1011 -- 1012.