Purdue University

Commands

• annotate
• combineMUMs
• delta-filter
• delta2vcf
• dnadiff
• exact-tandems
• mummer
• mummerplot
• nucmer
• promer
• repeat-match
• show-aligns
• show-coords
• show-diff
• show-snps
• show-tiling

Module

You can load the modules by:

module load biocontainers
module load mummer4

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Mummer4 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mummer4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mummer4

mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums