SMALT and SSAHA2

SMALT efficiently aligns DNA sequencing reads with a reference genome.
SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

Download

wget ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.7.2.tgz
wget ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_v2.5.5_x86_64.tgz
tar -zxvf smalt-0.7.2.tgz 
tar -zvxf ssaha2_v2.5.5_x86_64.tgz

Install

mv smalt-0.7.2 /usr/local/bin/ 
mv ssaha2_v2.5.5_x86_64 /usr/local/bin/ 
cd /usr/local/bin/
ln -s smalt-0.7.2/smalt_x86_64 smalt 
ln -s ssaha2_v2.5.5_x86_64/ssaha2 ssaha2
ln -s ssaha2_v2.5.5_x86_64/ssaha2Build ssaha2Build
ln -s ssaha2_v2.5.5_x86_64/ssahaSNP ssahaSNP 
chown -R root:root smalt-0.7.2
chown -R root:root ssaha2_v2.5.5_x86_64