mummer

Genetics

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.


Info

Module Name

mummer

Last Updated On

08/29/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

http://mummer.sourceforge.net

Documentation

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.

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 small,large,ram256g,ram1t
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

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

Agate Modules

Default

4.0.0.beta2

Other Modules

3.23.64bit, 3.23.CentOS7, 4.0.0.beta2, 3.23, 3.23_20151022

Mangi Modules

Default

4.0.0.beta2

Other Modules

3.23.64bit, 3.23.CentOS7, 4.0.0.beta2, 3.23, 3.23_20151022

Mesabi Modules

Default

4.0.0.beta2

Other Modules

3.23.64bit, 3.23.CentOS7, 4.0.0.beta2, 3.23, 3.23_20151022