mummer

Summary

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