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,
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.