LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by high-throughput sequencing technologies such as Roche 454.
LASTZ is available as a module on Apocrita.
To run the default installed version of LASTZ, simply load the
module load lastz lastz -h
For full usage documentation, run
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 1 #$ -l h_vmem=1G #$ -l h_rt=1:0:0 module load lastz lastz example1.fasta example2.fasta > output