MUMmer

MUMmer is a versatile alignment tool for DNA and protein sequences. It is commonly used for rapidly aligning whole genomes, comparing assemblies and detecting structural differences. On Roihu it is provided as MUMmer 4, which includes tools such as nucmer, promer, mummer, dnadiff and show-coords.

• MUMmer
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source. See the MUMmer repository.

Available

• Roihu: 4.0.1 (module mummer4), via the bio-apps module.

Usage

MUMmer is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MUMmer module:

module load bio-apps/v202603
module load mummer4/4.0.1

For example, to align a query genome against a reference with nucmer and summarise the alignment coordinates:

nucmer --threads 8 -p out reference.fa query.fa
show-coords -r out.delta > out.coords

Example batch script

#!/bin/bash
#SBATCH --job-name=mummer
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load mummer4/4.0.1

nucmer --threads $SLURM_CPUS_PER_TASK -p out reference.fa query.fa
show-coords -r out.delta > out.coords

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• MUMmer home page
• MUMmer GitHub repository

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