MUMmer is a system for rapidly aligning entire genomes.

Reference:

• MUMmer4: A fast and versatile genome alignment system. PLoS computational biology. Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. 2018 Jan 26;14(1):e1005944.
• Versatile and open software for comparing large genomes. S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg. Genome Biology (2004), 5:R12.

• MUMmer Manual

• Module Name: mummer (see the modules page for more information)
• Multithreaded.
• For MUMmer v3, mummerplot fails with any gnuplot later than 4.6.5. So you should 'module load gnuplot/4.6.5' before running mummerplot.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=50g --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 46116226]$ module load mummer

[user@cn3144 46116226]$ cp $MUMMER_TEST_DATA/*.gz .

[user@cn3144 46116226]$ gunzip *.gz

[user@cn3144 46116226]$ mummer chr_all.fa chrX.fa

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. MUMmer.sh). For example:

#!/bin/bash
set -e
module load mummer
mummer /fdb/genome/hg19/chr_all.fa input.fa

Submit this job using the Slurm sbatch command.

sbatch --mem=40g MUMmer.sh

Create a swarmfile (e.g. MUMmer.swarm). For example:

nucmer  /fdb/genome/hg19/chr_all.fa -p out1 file1.fa
nucmer  /fdb/genome/hg19/chr_all.fa -p out2 file2.fa
nucmer  /fdb/genome/hg19/chr_all.fa -p out3 file3.fa

Submit this job using the swarm command.

swarm -f MUMmer.swarm -g 20 [-t #] --module mummer