A spliced read mapper for RNA-Seq.
wget http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.Linux_x86_64.tar.gz tar xvzf tophat-1.4.1.Linux_x86_64.tar.gz
mv tophat-1.4.1.Linux_x86_64 /usr/local/bin/ ln -s /usr/local/bin/tophat-1.4.1.Linux_x86_64/tophat /usr/local/bin/
wget http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz tar zxvf test_data.tar.gz cd test_data/ tophat -r 20 test_ref reads_1.fq reads_2.fq