Mauve is a genomic sequence alignment program designed to align multiple genomic sequences when there are large-scale evolutionary events that need to also be considered when computing said alignments. These events can include things such as rearrangement and inversion, among others.

Using Mauve on RCC Resources

Before running Mauve, the gnu module must be loaded:

$ module load gnu

Mauve Command Line Tools in Serial

Mauve also has two command line tools, mauveAligner and progressiveMauve, both of which are sequence alignment tools. These can be run in serial using the command:

$ mauveAligner TEST1.seq

In the above example, TEST1.seq is a genomic sequence file which can be in one of three formats: FastA, Multi-FastA or GenBank. Note that you can have more than one sequence file in the command line arguments. See the Mauve Aligner documentation for more information.

Mauve Command Line Tools in Parallel

To speed up alignments, Mauve can be run in parallel using the GNU OpenMPI module. To load this module, simply type module load gnu openmpi.

A Slurm script can be written to do this as well. An example script is below, which uses 4 processors. Replace TEST with the name of your sequence file.

#!/bin/bash

#SBATCH -J Mauve_Test
#SBATCH -n 4
#SBATCH -p genacc_q
#SBATCH -t 00:10:00
#SBATCH --mail-type=ALL

module load gnu openmpi
mpirun -np 4 mauveAligner TEST.seq

Then submit your script using the following command, replacing YOURSCRIPT with the name of your script file:

$ sbatch YOURSCRIPT.sh

For detailed usage information about Mauve, refer to the official website.