# mummer

## Summary

+ **Module Name:** mummer
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://mummer.sourceforge.net](http://mummer.sourceforge.net)

## Software Description

MUMmer is a system for rapidly aligning entire genomes, whether in
complete or draft form. MUMmer can also align incomplete genomes- it can
easily handle the 100s or 1000s of contigs from a shotgun sequencing
project, and will align them to another set of contigs or a genome using
the NUCmer program included with the system.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load mummer

Depending on where you are working, there may be more than one version of mummer available.
To see which modules are available for loading you can run:

	module avail mummer
## Slurm Example


	#!/bin/bash
	#SBATCH --job-name="rfm_RunMUMMERTest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunMUMMERTest_job.out
	#SBATCH --error=rfm_RunMUMMERTest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load mummer/3.23
	wget https://public.s3.msi.umn.edu/reframe/sw/mummer/ref.fa
	wget https://public.s3.msi.umn.edu/reframe/sw/mummer/query.fa
	mummer -L -maxmatch ref.fa query.fa